-
Notifications
You must be signed in to change notification settings - Fork 2
/
3dtj_refine_001.log
1686 lines (1385 loc) · 69.3 KB
/
3dtj_refine_001.log
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
# Date 2019-04-19 Time 09:00:28 CST +0800 (1555635628.47 s)
#phil __OFF__
Command line arguments: "3dtj.pdb" "3dtj.mtz" "main.number_of_macro_cycles=5" "--overwrite" "ncs_search.enabled=true" "optimize_xyz=true" "main.nproc=16"
HOST = pva_mbp
HOSTTYPE = unknown
MACHTYPE = x86_64
OSTYPE = darwin
VENDOR = apple
USER = pafonine
PID = 94264
-------------------------------------------------------------------------------
PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
Version: dev
Release tag: svn+SVN
User: pafonine
-------------------------------------------------------------------------------
phenix.refine: Macromolecular Structure Refinement
-------------------------------------------------------------------------------
Phenix developers include:
Paul Adams, Pavel Afonine, Gabor Bunkoczi, Tom Burnley, Vincent Chen,
Youval Dar, Ian Davis, Eli Draizen, Nathaniel Echols, Richard Gildea,
Piet Gros, Ralf Grosse-Kunstleve, Jeffrey Headd, Bradley Hintze, Li-Wei Hung,
Tom Ioerger, Dorothee Liebschner, Airlie McCoy, Erik McKee, Nigel Moriarty,
Robert Oeffner, Billy Poon, Randy Read, Jane Richardson, David Richardson,
Jim Sacchettini, Nicholas Sauter, Oleg Sobolev, Laurent Storoni,
Tom Terwilliger, Christopher Williams, Peter Zwart
Phenix home page:
http://www.phenix-online.org/
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Phenix components are copyrighted by:
- Lawrence Berkeley National Laboratory
- Los Alamos National Laboratory
- University of Cambridge
- Duke University
- Texas Agricultural Experiment Station &
Texas Engineering Experiment Station
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Major third-party components of Phenix include:
Python, wxWidgets, wxPython, Boost, SCons, Clipper,
CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS,
MUSCLE, KSDSSP, PULCHRA, ANTLRv3
Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------
Processing inputs. This may take a minute or two.
Command line parameter definitions:
refinement.main.number_of_macro_cycles = 5
refinement.pdb_interpretation.ncs_search.enabled = true
refinement.target_weights.optimize_xyz_weight = true
refinement.main.nproc = 16
No user-defined map coefficients or files defined; will use default map
outputs instead.
Working crystal symmetry after inspecting all inputs:
Unit cell: (51.603, 51.675, 51.797, 109.942, 108.484, 110.02)
Space group: P 1 (No. 1)
================================== X-ray data =================================
F-obs:
3dtj.mtz:FOBS,SIGFOBS
Miller array info: 3dtj.mtz:FOBS,SIGFOBS
Observation type: xray.amplitude
Type of data: double, size=2158
Type of sigmas: double, size=2158
Number of Miller indices: 2158
Anomalous flag: False
Unit cell: (51.603, 51.675, 51.797, 109.942, 108.484, 110.02)
Space group: P 1 (No. 1)
Systematic absences: 0
Centric reflections: 0
Resolution range: 29.6959 3.95827
Completeness in resolution range: 0.605839
Completeness with d_max=infinity: 0.604651
Wavelength: 1.0440
Number of F-obs in resolution range: 2158
Number of F-obs<0 (these reflections will be rejected): 0
Number of F-obs=0 (these reflections will be used in refinement): 0
Refinement resolution range: d_max = 29.6959
d_min = 3.9583
R-free flags:
3dtj.mtz:FreeR_flag
Miller array info: 3dtj.mtz:FreeR_flag
Observation type: None
Type of data: int, size=2158
Type of sigmas: None
Number of Miller indices: 2158
Anomalous flag: False
Unit cell: (51.603, 51.675, 51.797, 109.942, 108.484, 110.02)
Space group: P 1 (No. 1)
Systematic absences: 0
Centric reflections: 0
Resolution range: 29.6959 3.95827
Completeness in resolution range: 0.605839
Completeness with d_max=infinity: 0.604651
Wavelength: 1.0440
Test (R-free flags) flag value: 1
Number of work/free reflections by resolution:
work free %free
bin 1: 29.6967 - 8.4681 [217/342] 187 30 13.8%
bin 2: 8.4681 - 6.7473 [224/381] 200 24 10.7%
bin 3: 6.7473 - 5.9020 [225/347] 196 29 12.9%
bin 4: 5.9020 - 5.3658 [245/379] 216 29 11.8%
bin 5: 5.3658 - 4.9832 [212/338] 186 26 12.3%
bin 6: 4.9832 - 4.6906 [204/339] 182 22 10.8%
bin 7: 4.6906 - 4.4565 [220/378] 211 9 4.1%
bin 8: 4.4565 - 4.2631 [235/349] 215 20 8.5%
bin 9: 4.2631 - 4.0994 [235/393] 214 21 8.9%
bin 10: 4.0994 - 3.9583 [141/316] 132 9 6.4%
overall 1939 219 10.1%
*** Automatic customization **************************************************
nonbonded_weight=100.000
*******************************************************************************
Monomer Library directory:
"/Users/pafonine/phenix/modules/chem_data/mon_lib"
Total number of atoms: 2288
Number of models: 1
Model: ""
Number of chains: 4
Chain: "A"
Number of atoms: 572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 73, 572
Classifications: {'peptide': 73}
Link IDs: {'PTRANS': 4, 'TRANS': 68}
Chain: "B"
Number of atoms: 572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 73, 572
Classifications: {'peptide': 73}
Link IDs: {'PTRANS': 4, 'TRANS': 68}
Chain: "C"
Number of atoms: 572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 73, 572
Classifications: {'peptide': 73}
Link IDs: {'PTRANS': 4, 'TRANS': 68}
Chain: "D"
Number of atoms: 572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 73, 572
Classifications: {'peptide': 73}
Link IDs: {'PTRANS': 4, 'TRANS': 68}
Time building chain proxies: 0.60, per 1000 atoms: 0.26
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
selection = chain 'C'
selection = chain 'D'
}
Number of scatterers: 2288
At special positions: 0
Unit cell: (51.603, 51.675, 51.797, 109.942, 108.484, 110.02)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 20 16.00
O 436 8.00
N 396 7.00
C 1436 6.00
sf(0) = scattering factor at diffraction angle 0.
No array of experimental phases found.
******************************************************************
INFO: Some parts of this job will make use of multiple processors:
******************************************************************
nproc = 16
Please ask your system administrator for advice about this, in particular if
you run this job through a queuing system.
============================== Scattering factors =============================
----------X-ray scattering dictionary----------
Number of scattering types: 4
Type Number sf(0) Gaussians
S 20 15.91 1
O 436 7.97 1
N 396 6.97 1
C 1436 5.97 1
sf(0) = scattering factor at diffraction angle 0.
==================== Fixing bad ADP in input model (if any) ===================
========================== Anomalous scatterer groups =========================
All atoms refined with f_prime=0 and f_double_prime=0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : False - 3.50
Amimo acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 0.27
Conformation dependent library (CDL) restraints added in 75.3 milliseconds
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 552
Time building geometry restraints manager: 0.31 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.19 - 1.31: 427
1.31 - 1.44: 552
1.44 - 1.57: 1303
1.57 - 1.70: 10
1.70 - 1.82: 32
Bond restraints: 2324
Sorted by residual:
bond pdb=" CA ALA B 177 "
pdb=" CB ALA B 177 "
ideal model delta sigma weight residual
1.529 1.448 0.081 1.64e-02 3.72e+03 2.45e+01
bond pdb=" CA VAL A 165 "
pdb=" CB VAL A 165 "
ideal model delta sigma weight residual
1.539 1.597 -0.058 1.20e-02 6.94e+03 2.30e+01
bond pdb=" CA VAL B 165 "
pdb=" CB VAL B 165 "
ideal model delta sigma weight residual
1.539 1.591 -0.052 1.20e-02 6.94e+03 1.88e+01
bond pdb=" C ALA C 187 "
pdb=" N THR C 188 "
ideal model delta sigma weight residual
1.332 1.277 0.056 1.40e-02 5.10e+03 1.57e+01
bond pdb=" C LEU C 190 "
pdb=" O LEU C 190 "
ideal model delta sigma weight residual
1.236 1.188 0.049 1.25e-02 6.40e+03 1.53e+01
... (remaining 2319 not shown)
Histogram of bond angle deviations from ideal:
99.97 - 106.76: 98
106.76 - 113.54: 1216
113.54 - 120.33: 877
120.33 - 127.11: 931
127.11 - 133.90: 18
Bond angle restraints: 3140
Sorted by residual:
angle pdb=" N ILE C 150 "
pdb=" CA ILE C 150 "
pdb=" C ILE C 150 "
ideal model delta sigma weight residual
112.04 103.27 8.77 1.40e+00 5.10e-01 3.93e+01
angle pdb=" C LYS C 182 "
pdb=" N ASN C 183 "
pdb=" CA ASN C 183 "
ideal model delta sigma weight residual
120.44 127.80 -7.36 1.30e+00 5.92e-01 3.21e+01
angle pdb=" C GLY D 206 "
pdb=" N PRO D 207 "
pdb=" CA PRO D 207 "
ideal model delta sigma weight residual
119.89 125.28 -5.39 1.02e+00 9.61e-01 2.79e+01
angle pdb=" C LYS A 182 "
pdb=" N ASN A 183 "
pdb=" CA ASN A 183 "
ideal model delta sigma weight residual
120.44 126.99 -6.55 1.30e+00 5.92e-01 2.54e+01
angle pdb=" N ILE A 150 "
pdb=" CA ILE A 150 "
pdb=" C ILE A 150 "
ideal model delta sigma weight residual
113.07 106.37 6.70 1.36e+00 5.41e-01 2.42e+01
... (remaining 3135 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 27.84: 1330
27.84 - 55.68: 98
55.68 - 83.51: 11
83.51 - 111.35: 1
111.35 - 139.19: 4
Dihedral angle restraints: 1444
sinusoidal: 596
harmonic: 848
Sorted by residual:
dihedral pdb=" CB GLU B 175 "
pdb=" CG GLU B 175 "
pdb=" CD GLU B 175 "
pdb=" OE1 GLU B 175 "
ideal model delta sinusoidal sigma weight residual
0.00 139.19 -139.19 1 3.00e+01 1.11e-03 1.87e+01
dihedral pdb=" CB GLU D 175 "
pdb=" CG GLU D 175 "
pdb=" CD GLU D 175 "
pdb=" OE1 GLU D 175 "
ideal model delta sinusoidal sigma weight residual
0.00 137.22 -137.22 1 3.00e+01 1.11e-03 1.85e+01
dihedral pdb=" CB GLU A 175 "
pdb=" CG GLU A 175 "
pdb=" CD GLU A 175 "
pdb=" OE1 GLU A 175 "
ideal model delta sinusoidal sigma weight residual
0.00 127.96 -127.96 1 3.00e+01 1.11e-03 1.72e+01
... (remaining 1441 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.055: 159
0.055 - 0.110: 124
0.110 - 0.164: 53
0.164 - 0.219: 16
0.219 - 0.274: 4
Chirality restraints: 356
Sorted by residual:
chirality pdb=" CG LEU C 190 "
pdb=" CB LEU C 190 "
pdb=" CD1 LEU C 190 "
pdb=" CD2 LEU C 190 "
both_signs ideal model delta sigma weight residual
False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00
chirality pdb=" CA ILE C 150 "
pdb=" N ILE C 150 "
pdb=" C ILE C 150 "
pdb=" CB ILE C 150 "
both_signs ideal model delta sigma weight residual
False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00
chirality pdb=" CB VAL C 191 "
pdb=" CA VAL C 191 "
pdb=" CG1 VAL C 191 "
pdb=" CG2 VAL C 191 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00
... (remaining 353 not shown)
Planarity restraints: 408
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C GLU D 159 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.54e+00
pdb=" N PRO D 160 " 0.102 5.00e-02 4.00e+02
pdb=" CA PRO D 160 " -0.030 5.00e-02 4.00e+02
pdb=" CD PRO D 160 " -0.033 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CB TYR B 169 " 0.026 2.00e-02 2.50e+03 1.30e-02 3.36e+00
pdb=" CG TYR B 169 " -0.015 2.00e-02 2.50e+03
pdb=" CD1 TYR B 169 " -0.012 2.00e-02 2.50e+03
pdb=" CD2 TYR B 169 " -0.011 2.00e-02 2.50e+03
pdb=" CE1 TYR B 169 " -0.002 2.00e-02 2.50e+03
pdb=" CE2 TYR B 169 " -0.003 2.00e-02 2.50e+03
pdb=" CZ TYR B 169 " 0.008 2.00e-02 2.50e+03
pdb=" OH TYR B 169 " 0.010 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR A 169 " 0.022 2.00e-02 2.50e+03 1.25e-02 3.14e+00
pdb=" CG TYR A 169 " -0.022 2.00e-02 2.50e+03
pdb=" CD1 TYR A 169 " -0.009 2.00e-02 2.50e+03
pdb=" CD2 TYR A 169 " -0.008 2.00e-02 2.50e+03
pdb=" CE1 TYR A 169 " 0.003 2.00e-02 2.50e+03
pdb=" CE2 TYR A 169 " 0.001 2.00e-02 2.50e+03
pdb=" CZ TYR A 169 " 0.011 2.00e-02 2.50e+03
pdb=" OH TYR A 169 " 0.002 2.00e-02 2.50e+03
... (remaining 405 not shown)
Histogram of nonbonded interaction distances:
2.29 - 2.81: 593
2.81 - 3.34: 2429
3.34 - 3.86: 4144
3.86 - 4.38: 4963
4.38 - 4.90: 7828
Nonbonded interactions: 19957
Sorted by model distance:
nonbonded pdb=" O VAL B 221 "
pdb=" CG1 VAL B 221 "
model vdw
2.292 3.460
nonbonded pdb=" O VAL A 221 "
pdb=" CG1 VAL A 221 "
model vdw
2.293 3.460
nonbonded pdb=" O GLY D 220 "
pdb=" CB VAL D 221 "
model vdw
2.300 3.470
nonbonded pdb=" N ILE C 150 "
pdb=" N LEU C 151 "
model vdw
2.440 2.560
nonbonded pdb=" O PRO D 160 "
pdb=" C PHE D 161 "
model vdw
2.478 3.270
... (remaining 19952 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
======================== Summary of geometry restraints =======================
====================== Modifying start model if requested =====================
n_use = 2288
n_use_u_iso = 2288
n_use_u_aniso = 0
n_grad_site = 0
n_grad_u_iso = 0
n_grad_u_aniso = 0
n_grad_occupancy = 0
n_grad_fp = 0
n_grad_fdp = 0
total number of scatterers = 2288
================== Extract refinement strategy and selections =================
Refinement flags and selection counts:
individual_sites = True (2288 atoms)
torsion_angles = False (0 atoms)
rigid_body = False (0 atoms in 0 groups)
individual_adp = True (iso = 2288 aniso = 0)
group_adp = False (0 atoms in 0 groups)
tls = False (0 atoms in 0 groups)
occupancies = True (0 atoms)
group_anomalous = False
*******************************************************************************
Automatic adjustment:
hydrogens.refine=riding
*******************************************************************************
==================== Process input NCS or/and find new NCS ====================
Number of NCS groups: 1
refinement.pdb_interpretation.ncs_group {
reference = chain 'A'
selection = chain 'B'
selection = chain 'C'
selection = chain 'D'
}
Not restraining NCS-related b-factors:
refinement.ncs.b_factor_weight = 0.0
Determining NCS matches...
--------------------------------------------------------
Torsion NCS Matching Summary:
SER A 149 <=> SER B 149 <=> SER C 149 <=> SER D 149
ILE A 150 <=> ILE B 150 <=> ILE C 150 <=> ILE D 150
LEU A 151 <=> LEU B 151 <=> LEU C 151 <=> LEU D 151
ASP A 152 <=> ASP B 152 <=> ASP C 152 <=> ASP D 152
ILE A 153 <=> ILE B 153 <=> ILE C 153 <=> ILE D 153
ARG A 154 <=> ARG B 154 <=> ARG C 154 <=> ARG D 154
GLN A 155 <=> GLN B 155 <=> GLN C 155 <=> GLN D 155
GLY A 156 <=> GLY B 156 <=> GLY C 156 <=> GLY D 156
PRO A 157 <=> PRO B 157 <=> PRO C 157 <=> PRO D 157
LYS A 158 <=> LYS B 158 <=> LYS C 158 <=> LYS D 158
GLU A 159 <=> GLU B 159 <=> GLU C 159 <=> GLU D 159
PRO A 160 <=> PRO B 160 <=> PRO C 160 <=> PRO D 160
PHE A 161 <=> PHE B 161 <=> PHE C 161 <=> PHE D 161
ARG A 162 <=> ARG B 162 <=> ARG C 162 <=> ARG D 162
ASP A 163 <=> ASP B 163 <=> ASP C 163 <=> ASP D 163
TYR A 164 <=> TYR B 164 <=> TYR C 164 <=> TYR D 164
VAL A 165 <=> VAL B 165 <=> VAL C 165 <=> VAL D 165
ASP A 166 <=> ASP B 166 <=> ASP C 166 <=> ASP D 166
ARG A 167 <=> ARG B 167 <=> ARG C 167 <=> ARG D 167
PHE A 168 <=> PHE B 168 <=> PHE C 168 <=> PHE D 168
TYR A 169 <=> TYR B 169 <=> TYR C 169 <=> TYR D 169
LYS A 170 <=> LYS B 170 <=> LYS C 170 <=> LYS D 170
THR A 171 <=> THR B 171 <=> THR C 171 <=> THR D 171
LEU A 172 <=> LEU B 172 <=> LEU C 172 <=> LEU D 172
ARG A 173 <=> ARG B 173 <=> ARG C 173 <=> ARG D 173
ALA A 174 <=> ALA B 174 <=> ALA C 174 <=> ALA D 174
GLU A 175 <=> GLU B 175 <=> GLU C 175 <=> GLU D 175
GLN A 176 <=> GLN B 176 <=> GLN C 176 <=> GLN D 176
ALA A 177 <=> ALA B 177 <=> ALA C 177 <=> ALA D 177
SER A 178 <=> SER B 178 <=> SER C 178 <=> SER D 178
GLN A 179 <=> GLN B 179 <=> GLN C 179 <=> GLN D 179
GLU A 180 <=> GLU B 180 <=> GLU C 180 <=> GLU D 180
VAL A 181 <=> VAL B 181 <=> VAL C 181 <=> VAL D 181
LYS A 182 <=> LYS B 182 <=> LYS C 182 <=> LYS D 182
ASN A 183 <=> ASN B 183 <=> ASN C 183 <=> ASN D 183
TRP A 184 <=> TRP B 184 <=> TRP C 184 <=> TRP D 184
MET A 185 <=> MET B 185 <=> MET C 185 <=> MET D 185
THR A 186 <=> THR B 186 <=> THR C 186 <=> THR D 186
ALA A 187 <=> ALA B 187 <=> ALA C 187 <=> ALA D 187
THR A 188 <=> THR B 188 <=> THR C 188 <=> THR D 188
LEU A 189 <=> LEU B 189 <=> LEU C 189 <=> LEU D 189
LEU A 190 <=> LEU B 190 <=> LEU C 190 <=> LEU D 190
VAL A 191 <=> VAL B 191 <=> VAL C 191 <=> VAL D 191
GLN A 192 <=> GLN B 192 <=> GLN C 192 <=> GLN D 192
ASN A 193 <=> ASN B 193 <=> ASN C 193 <=> ASN D 193
ALA A 194 <=> ALA B 194 <=> ALA C 194 <=> ALA D 194
ASN A 195 <=> ASN B 195 <=> ASN C 195 <=> ASN D 195
PRO A 196 <=> PRO B 196 <=> PRO C 196 <=> PRO D 196
ASP A 197 <=> ASP B 197 <=> ASP C 197 <=> ASP D 197
CYS A 198 <=> CYS B 198 <=> CYS C 198 <=> CYS D 198
LYS A 199 <=> LYS B 199 <=> LYS C 199 <=> LYS D 199
THR A 200 <=> THR B 200 <=> THR C 200 <=> THR D 200
ILE A 201 <=> ILE B 201 <=> ILE C 201 <=> ILE D 201
LEU A 202 <=> LEU B 202 <=> LEU C 202 <=> LEU D 202
LYS A 203 <=> LYS B 203 <=> LYS C 203 <=> LYS D 203
ALA A 204 <=> ALA B 204 <=> ALA C 204 <=> ALA D 204
LEU A 205 <=> LEU B 205 <=> LEU C 205 <=> LEU D 205
GLY A 206 <=> GLY B 206 <=> GLY C 206 <=> GLY D 206
PRO A 207 <=> PRO B 207 <=> PRO C 207 <=> PRO D 207
GLY A 208 <=> GLY B 208 <=> GLY C 208 <=> GLY D 208
ALA A 209 <=> ALA B 209 <=> ALA C 209 <=> ALA D 209
THR A 210 <=> THR B 210 <=> THR C 210 <=> THR D 210
LEU A 211 <=> LEU B 211 <=> LEU C 211 <=> LEU D 211
GLU A 212 <=> GLU B 212 <=> GLU C 212 <=> GLU D 212
GLU A 213 <=> GLU B 213 <=> GLU C 213 <=> GLU D 213
MET A 214 <=> MET B 214 <=> MET C 214 <=> MET D 214
MET A 215 <=> MET B 215 <=> MET C 215 <=> MET D 215
THR A 216 <=> THR B 216 <=> THR C 216 <=> THR D 216
ALA A 217 <=> ALA B 217 <=> ALA C 217 <=> ALA D 217
CYS A 218 <=> CYS B 218 <=> CYS C 218 <=> CYS D 218
GLN A 219 <=> GLN B 219 <=> GLN C 219 <=> GLN D 219
GLY A 220 <=> GLY B 220 <=> GLY C 220 <=> GLY D 220
VAL A 221 <=> VAL B 221 <=> VAL C 221 <=> VAL D 221
--------------------------------------------------------
Initializing torsion NCS restraints...
Number of torsion NCS restraints: 1410
=================== Write initial parameters into .eff file ===================
Writing effective parameters to file:
/Users/pafonine/Desktop/QR2019April/low_high_res_pair/3dtj_refine_001.eff
Writing geometry restraints to file:
/Users/pafonine/Desktop/QR2019April/low_high_res_pair/3dtj_refine_001.geo
CPU time processing inputs: 9.23
============================ Non-default parameters ===========================
A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.
#phil __ON__
refinement {
crystal_symmetry {
unit_cell = 51.60300064 51.67499924 51.79700089 109.9420013 108.4840012 \
110.0199966
space_group = "P 1"
}
input {
pdb {
file_name = "3dtj.pdb"
}
xray_data {
file_name = "3dtj.mtz"
labels = "FOBS,SIGFOBS"
r_free_flags {
file_name = "3dtj.mtz"
label = "FreeR_flag"
test_flag_value = 1
}
}
}
output {
prefix = "3dtj_refine"
serial = 1
}
electron_density_maps {
map_coefficients {
map_type = "2mFo-DFc"
mtz_label_amplitudes = "2FOFCWT"
mtz_label_phases = "PH2FOFCWT"
fill_missing_f_obs = True
}
map_coefficients {
map_type = "2mFo-DFc"
mtz_label_amplitudes = "2FOFCWT_no_fill"
mtz_label_phases = "PH2FOFCWT_no_fill"
}
map_coefficients {
map_type = "mFo-DFc"
mtz_label_amplitudes = "FOFCWT"
mtz_label_phases = "PHFOFCWT"
}
map_coefficients {
map_type = "anomalous"
mtz_label_amplitudes = "ANOM"
mtz_label_phases = "PANOM"
}
map {
map_type = "2mFo-DFc"
fill_missing_f_obs = True
}
map {
map_type = "2mFo-DFc"
}
map {
map_type = "mFo-DFc"
}
}
main {
number_of_macro_cycles = 5
nproc = 16
}
hydrogens {
refine = individual *riding Auto
}
ncs {
b_factor_weight = 0
}
pdb_interpretation {
nonbonded_weight = 100
ncs_group {
reference = "chain A"
selection = "chain B"
selection = "chain C"
selection = "chain D"
}
ncs_search {
enabled = True
chain_max_rmsd = 999
residue_match_radius = 999
}
}
target_weights {
optimize_xyz_weight = True
}
}
#phil __OFF__
=============================== refinement start ==============================
----------structure factors based statistics (before refinement)----------
----------X-ray data----------
|--(resolution: 3.96 - 29.70 A, n_refl.=2158 (all), 10.15 % free)-------------|
| |
| r_work= 0.4273 r_free= 0.4441 coordinate error (max.-lik. estimate): 0.38 A |
| |
| normalized target function (ml) (work): 5.356112 |
| target function (ml) not normalized (work): 10385.500695 |
| target function (ml) not normalized (free): 1192.129502 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets |
|number range work test work test work test|
| 1: 29.6967 - 4.9832 0.63 985 138 0.4526 0.4415 5.6954 5.6968|
| 2: 4.9832 - 3.9583 0.58 954 81 0.3787 0.4529 5.0058 5.012|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
| |
| Bin Resolution No. Refl. FOM Phase Scale Alpha Beta |
| # range work test error factor |
| 1: 29.6967 - 4.9832 985 138 0.55 48.68 1.00 0.54 25141.24|
| 2: 4.9832 - 3.9583 954 81 0.66 39.87 0.99 0.57 3900.88|
|alpha: min = 0.40 max = 0.85 mean = 0.56|
|beta: min = 2396.33 max = 99095.03 mean = 14690.85|
|figures of merit: min = 0.00 max = 0.99 mean = 0.60|
|phase err.(work): min = 7.25 max = 89.82 mean = 44.34|
|phase err.(test): min = 10.60 max = 87.18 mean = 47.28|
|-----------------------------------------------------------------------------|
----------Initial model statistics (before refinement)----------
min max mean <Bi,j> iso aniso
Overall: 20.00 80.94 59.55 3.58 2288 0
Protein: 20.00 80.94 59.55 3.58 2288 0
Chain A: 20.00 80.15 59.55 N/A 572 0
Chain C: 20.00 80.05 59.57 N/A 572 0
Chain B: 20.00 80.71 59.54 N/A 572 0
Chain D: 20.00 80.94 59.53 N/A 572 0
Histogram:
Values Number of atoms
20.00 - 26.09 44
26.09 - 32.19 0
32.19 - 38.28 0
38.28 - 44.38 1
44.38 - 50.47 102
50.47 - 56.56 713
56.56 - 62.66 563
62.66 - 68.75 578
68.75 - 74.85 212
74.85 - 80.94 75
|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 |
|-----------------------------------------------------------------------------|
*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************
|--(resolution: 3.96 - 29.70 A, n_refl.=2158 (all), 10.15 % free)-------------|
| |
| r_work= 0.4273 r_free= 0.4441 coordinate error (max.-lik. estimate): 0.38 A |
| |
| normalized target function (ml) (work): 5.356112 |
| target function (ml) not normalized (work): 10385.500695 |
| target function (ml) not normalized (free): 1192.129502 |
|-----------------------------------------------------------------------------|
=========================== Bulk-solvent and scaling ==========================
============================= updating all scales =============================
start: r(all,work,free)=0.4295 0.4273 0.4441 n_refl.: 2158
re-set all scales: r(all,work,free)=0.4295 0.4273 0.4441 n_refl.: 2158
remove outliers: r(all,work,free)=0.4292 0.4270 0.4441 n_refl.: 2154
overall B=83.35 to atoms: r(all,work,free)=0.5178 0.5266 0.4238 n_refl.: 2154
bulk-solvent and scaling: r(all,work,free)=0.3252 0.3231 0.3426 n_refl.: 2154
remove outliers: r(all,work,free)=0.3252 0.3231 0.3426 n_refl.: 2154
======================== Statistics in resolution bins ========================
Total model structure factor:
F_model = k_total * (F_calc + k_mask * F_mask)
k_total = k_isotropic * k_anisotropic
Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani kmask
29.696-11.724 76.34 87 13 0.2385 368.129 359.988 1.183 1.023 0.294
11.706-8.777 53.76 83 17 0.2238 304.865 290.270 1.098 1.031 0.243
8.763-6.561 59.59 240 24 0.3340 176.598 172.910 1.040 1.007 0.203
6.558-4.910 63.73 625 85 0.3535 107.416 100.666 0.964 0.974 0.139
4.910-3.958 58.23 900 80 0.3580 84.898 78.569 1.092 0.931 0.077
Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
k_overall=1.0047 b_overall=0.3912
============================ Set refinement target ============================
using refinement target ls_wunit_k1
================================== NQH flips ==================================
r_work=0.3231 r_free=0.3426
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 179 GLN
C 179 GLN
C 192 GLN
** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 3
r_work=0.3230 r_free=0.3423
========================= Global real-space refinement ========================
|-real space refinement (target=simple)---------------------------------------|
| start: r_work=0.3230 r_free=0.3423 rmsd: bonds=0.015 angles= 1.50 |
| final: r_work=0.3031 r_free=0.3480 rmsd: bonds=0.004 angles= 0.66 |
| --------------------------------------------------------------------------- |
==================== Compute data/restraints target weights ===================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc |
| wxc = 13.865171 wxc_scale = 0.500 wc = 1.000 |
| |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu |
| wxu = 0.091501 wxu_scale = 1.000 wu = 1.000 |
|-----------------------------------------------------------------------------|
====================== XYZ individual (reciprocal space) ======================
----------Updating torsion NCS restraints----------
Verifying torsion NCS restraints...
Number of torsion NCS restraints: 1450
R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS
work free delta bonds angl data restr
30.31 34.80 4.50 0.004 0.7 7.2 0.0 2.4 0 none 0.094 0.1239
30.48 34.24 3.76 0.002 0.6 6.5 0.0 2.4 0 0.125 0.096 0.1036
30.30 34.16 3.86 0.003 0.6 6.5 0.0 2.4 0 0.250 0.094 0.1038
29.92 34.16 4.24 0.003 0.6 6.5 0.0 2.4 0 0.500 0.091 0.1053
29.12 34.27 5.15 0.004 0.6 5.0 0.0 1.6 0 1.000 0.085 0.1105
27.98 34.35 6.36 0.005 0.7 4.8 0.0 1.6 0 2.000 0.076 0.1221
27.12 34.73 7.61 0.006 0.8 4.8 0.0 1.6 0 3.000 0.070 0.1382
26.48 34.89 8.41 0.007 0.9 5.7 0.0 2.0 0 4.000 0.067 0.1505
25.96 34.88 8.91 0.008 0.9 6.1 0.0 2.0 0 5.000 0.064 0.1635
25.51 35.25 9.74 0.009 1.0 6.3 0.0 2.0 0 6.000 0.062 0.1779
25.23 35.19 9.96 0.009 1.1 7.0 0.0 2.0 0 7.000 0.061 0.1870
24.99 35.27 10.28 0.010 1.1 7.2 0.0 2.0 0 8.000 0.060 0.1995
24.61 35.29 10.68 0.011 1.2 7.8 0.0 2.0 0 9.000 0.058 0.2140
24.54 35.15 10.61 0.011 1.2 8.3 0.0 2.0 0 10.000 0.058 0.2209
25.25 35.23 9.98 0.009 1.1 7.2 0.0 2.0 0 6.933 0.061 0.1863
Best XYZ weight: 0.125
Updating mask...
Accepted refinement result:
30.48 34.24 3.76 0.002 0.6 6.5 0.0 2.4 0 0.125 0.096 0.1036
Legend:
- first line corresponds to starting state (before refinement)
- R-factors reported in percent
- delta is Rfree-Rwork in percent
- CLASH is all-atom Molprobity clashscore
- ROTA is percent of side-chain rotamer outliers
- RAMA is percent of Ramachandran plot outliers
- CBET is number of Cbeta deviations
- WEIGHT is relative weight between X-ray (or neutron) target and restraints
- TARGETS: the values of X-ray (or neutron) and restraints target functions
====================== ADP refinement (reciprocal space) ======================
----------Individual ADP refinement----------
R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS
work free delta data restr
30.48 34.24 3.76 3.580 142.894 0.092 0.096
27.42 33.44 6.03 5.216 146.017 0.092 0.077
min max mean <Bi,j> iso aniso
Overall: 122.35 201.84 146.02 5.22 2288 0
Protein: 122.35 201.84 146.02 5.22 2288 0
Chain A: 125.09 191.67 146.84 N/A 572 0
Chain C: 125.79 201.84 145.93 N/A 572 0
Chain B: 125.35 187.80 145.28 N/A 572 0
Chain D: 122.35 189.74 146.01 N/A 572 0
Histogram:
Values Number of atoms
122.35 - 130.30 75
130.30 - 138.25 484
138.25 - 146.20 761
146.20 - 154.15 528
154.15 - 162.09 241
162.09 - 170.04 120
170.04 - 177.99 54
177.99 - 185.94 16
185.94 - 193.89 8
193.89 - 201.84 1
*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************
|--(resolution: 3.96 - 29.70 A, n_refl.=2154 (all), 10.17 % free)-------------|
| |
| r_work= 0.2742 r_free= 0.3344 coordinate error (max.-lik. estimate): 0.24 A |
| |
| normalized target function (ls_wunit_k1) (work): 0.076805 |
| target function (ls_wunit_k1) not normalized (work): 148.617023 |
| target function (ls_wunit_k1) not normalized (free): 27.359025 |
|-----------------------------------------------------------------------------|
=========================== Bulk-solvent and scaling ==========================
============================= updating all scales =============================
start: r(all,work,free)=0.2815 0.2742 0.3344 n_refl.: 2154
re-set all scales: r(all,work,free)=0.4900 0.4948 0.4331 n_refl.: 2154
remove outliers: r(all,work,free)=0.4900 0.4948 0.4331 n_refl.: 2154
overall B=-17.28 to atoms: r(all,work,free)=0.4561 0.4592 0.4222 n_refl.: 2154
bulk-solvent and scaling: r(all,work,free)=0.2772 0.2692 0.3296 n_refl.: 2154
remove outliers: r(all,work,free)=0.2772 0.2692 0.3296 n_refl.: 2154
======================== Statistics in resolution bins ========================
Total model structure factor:
F_model = k_total * (F_calc + k_mask * F_mask)
k_total = k_isotropic * k_anisotropic
Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani kmask
29.696-11.724 76.34 87 13 0.1918 368.129 355.820 1.140 1.006 0.275
11.706-8.777 53.76 83 17 0.1644 304.865 291.647 1.152 1.027 0.240
8.763-6.561 59.59 240 24 0.2414 176.598 178.292 1.101 1.016 0.238
6.558-4.910 63.73 625 85 0.3048 107.416 102.852 0.954 1.004 0.173
4.910-3.958 58.23 900 80 0.3207 84.898 82.603 1.005 0.992 0.088
Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
k_overall=1.0577 b_overall=5.2799
============================ Set refinement target ============================
using refinement target ls_wunit_k1
============================ Update CDL restraints ============================
================================== NQH flips ==================================
r_work=0.2692 r_free=0.3296
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
r_work=0.2692 r_free=0.3296
========================= Local real-space refinement =========================
Before:
r_work=0.2692 r_free=0.3296
rotamer outliers: 2.42 %
After:
r_work=0.2694 r_free=0.3309
rotamer outliers: 0.00 %
==================== Compute data/restraints target weights ===================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc |
| wxc = 20.213507 wxc_scale = 0.023 wc = 1.000 |
| |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu |
| wxu = 0.101290 wxu_scale = 1.000 wu = 1.000 |
|-----------------------------------------------------------------------------|
====================== XYZ individual (reciprocal space) ======================
----------Updating torsion NCS restraints----------
Verifying torsion NCS restraints...
Number of torsion NCS restraints: 880
R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS
work free delta bonds angl data restr
26.94 33.09 6.15 0.002 0.6 6.8 0.0 0.0 0 none 0.073 0.0528
27.05 33.16 6.11 0.002 0.5 6.1 0.0 0.0 0 0.047 0.073 0.0452
26.89 33.10 6.22 0.002 0.5 5.9 0.0 0.0 0 0.140 0.072 0.0454
26.64 32.94 6.30 0.002 0.5 5.7 0.0 0.8 0 0.279 0.071 0.0459
26.44 32.84 6.40 0.002 0.5 5.2 0.0 0.8 0 0.419 0.070 0.0466
26.21 32.90 6.69 0.002 0.5 4.8 0.0 0.8 0 0.558 0.068 0.0474
25.97 32.83 6.86 0.003 0.5 4.4 0.0 0.8 0 0.698 0.066 0.0486
25.83 32.71 6.88 0.003 0.6 3.9 0.0 0.4 0 0.837 0.066 0.0497
25.67 32.51 6.84 0.003 0.6 4.1 0.0 0.4 0 0.977 0.065 0.0512
26.37 32.91 6.54 0.002 0.5 4.8 0.0 0.8 0 0.465 0.069 0.0469
Best XYZ weight: 0.047
Updating mask...
Accepted refinement result:
27.05 33.16 6.11 0.002 0.5 6.1 0.0 0.0 0 0.047 0.073 0.0452
Legend:
- first line corresponds to starting state (before refinement)
- R-factors reported in percent
- delta is Rfree-Rwork in percent
- CLASH is all-atom Molprobity clashscore
- ROTA is percent of side-chain rotamer outliers
- RAMA is percent of Ramachandran plot outliers
- CBET is number of Cbeta deviations
- WEIGHT is relative weight between X-ray (or neutron) target and restraints
- TARGETS: the values of X-ray (or neutron) and restraints target functions
===================== Post-minimization rotamer correction ====================
Before:
r_work=0.2705 r_free=0.3316
rotamer outliers: 0.00 %
outliers start: 0
tune up