Starting phenix.real_space_refine on Mon Jun 23 04:01:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7smp_25204/06_2025/7smp_25204_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7smp_25204/06_2025/7smp_25204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7smp_25204/06_2025/7smp_25204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7smp_25204/06_2025/7smp_25204.map" model { file = "/net/cci-nas-00/data/ceres_data/7smp_25204/06_2025/7smp_25204_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7smp_25204/06_2025/7smp_25204_trim.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 83 5.16 5 C 8573 2.51 5 N 2148 2.21 5 O 2318 1.98 5 H 13353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26477 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 13184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 13184 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 29, 'TRANS': 803} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 13216 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 29, 'TRANS': 805} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' K': 1, '82U': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' K': 1, '82U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.40, per 1000 atoms: 0.51 Number of scatterers: 26477 At special positions: 0 Unit cell: (84.53, 151.94, 124.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 83 16.00 O 2318 8.00 N 2148 7.00 C 8573 6.00 H 13353 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.04 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 7.21 Conformation dependent library (CDL) restraints added in 2.1 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 65.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.524A pdb=" N TRP B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.422A pdb=" N PHE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.255A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 397 removed outlier: 3.619A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 426 Processing helix chain 'B' and resid 427 through 455 Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.522A pdb=" N LYS B 461 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.727A pdb=" N GLY B 504 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 506 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 544 Proline residue: B 519 - end of helix Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.710A pdb=" N THR B 555 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 Processing helix chain 'B' and resid 575 through 579 Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.548A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 633 removed outlier: 3.667A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 639 through 643 removed outlier: 3.681A pdb=" N LYS B 643 " --> pdb=" O MET B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 669 removed outlier: 3.687A pdb=" N ALA B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 699 Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 731 through 752 removed outlier: 3.625A pdb=" N LEU B 736 " --> pdb=" O TRP B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 780 removed outlier: 3.577A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 811 removed outlier: 4.010A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 849 removed outlier: 4.239A pdb=" N MET B 832 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 834 " --> pdb=" O GLN B 830 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.627A pdb=" N VAL B 900 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1046 through 1050 removed outlier: 3.915A pdb=" N LYS B1050 " --> pdb=" O LYS B1047 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1079 Processing helix chain 'B' and resid 1097 through 1109 Processing helix chain 'B' and resid 1119 through 1129 Processing helix chain 'B' and resid 1136 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1191 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.696A pdb=" N PHE A 305 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 344 removed outlier: 3.699A pdb=" N ASN A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 361 through 398 removed outlier: 3.648A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.659A pdb=" N ALA A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 4.166A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 486 through 499 Proline residue: A 496 - end of helix removed outlier: 3.576A pdb=" N THR A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.421A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 542 Proline residue: A 519 - end of helix removed outlier: 3.526A pdb=" N SER A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.790A pdb=" N LEU A 570 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 599 through 632 removed outlier: 3.877A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix removed outlier: 3.531A pdb=" N ASP A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 removed outlier: 3.706A pdb=" N ALA A 642 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 643 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 643' Processing helix chain 'A' and resid 651 through 669 removed outlier: 3.575A pdb=" N ALA A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 699 Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.861A pdb=" N ASN A 731 " --> pdb=" O MET A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 Processing helix chain 'A' and resid 760 through 780 Processing helix chain 'A' and resid 797 through 800 Processing helix chain 'A' and resid 801 through 811 removed outlier: 4.060A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 849 removed outlier: 4.413A pdb=" N MET A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LYS A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 889 through 893 removed outlier: 4.553A pdb=" N LEU A 893 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.666A pdb=" N VAL A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Proline residue: A1040 - end of helix Processing helix chain 'A' and resid 1061 through 1063 No H-bonds generated for 'chain 'A' and resid 1061 through 1063' Processing helix chain 'A' and resid 1064 through 1079 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1119 through 1130 Processing helix chain 'A' and resid 1136 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1191 removed outlier: 3.774A pdb=" N SER A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 791 through 793 removed outlier: 6.651A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 821 " --> pdb=" O CYS B 791 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 793 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL B 823 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 822 " --> pdb=" O ALA B 856 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 883 through 887 removed outlier: 6.596A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE B1054 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N MET B1087 " --> pdb=" O ILE B1054 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL B1056 " --> pdb=" O MET B1087 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B1089 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B1058 " --> pdb=" O LEU B1089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1112 through 1113 Processing sheet with id=AA4, first strand: chain 'A' and resid 854 through 859 removed outlier: 6.511A pdb=" N MET A 818 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA A 856 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N CYS A 820 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A 858 " --> pdb=" O CYS A 820 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N HIS A 822 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY A 887 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU A1198 " --> pdb=" O ASN A1164 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A1166 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A1200 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A1168 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR A1023 " --> pdb=" O ALA A1163 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE A1165 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1169 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A1024 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE A1057 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A1026 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLY A1059 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A1089 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A1058 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1112 through 1113 783 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.51 Time building geometry restraints manager: 8.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13337 1.03 - 1.23: 55 1.23 - 1.42: 5511 1.42 - 1.62: 7728 1.62 - 1.82: 142 Bond restraints: 26773 Sorted by residual: bond pdb=" N 82U B1302 " pdb=" CA 82U B1302 " ideal model delta sigma weight residual 1.366 1.433 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N 82U A1301 " pdb=" CA 82U A1301 " ideal model delta sigma weight residual 1.366 1.433 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" N 82U B1301 " pdb=" CA 82U B1301 " ideal model delta sigma weight residual 1.366 1.432 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" NE1 82U A1301 " pdb=" S1 82U A1301 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" NE1 82U B1302 " pdb=" S1 82U B1302 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.34e+00 ... (remaining 26768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 48435 3.70 - 7.39: 66 7.39 - 11.09: 4 11.09 - 14.78: 4 14.78 - 18.48: 8 Bond angle restraints: 48517 Sorted by residual: angle pdb=" C 82U B1301 " pdb=" C1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 120.11 138.59 -18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" O1 82U B1302 " pdb=" S1 82U B1302 " pdb=" O2 82U B1302 " ideal model delta sigma weight residual 118.12 100.23 17.89 3.00e+00 1.11e-01 3.56e+01 angle pdb=" O1 82U A1301 " pdb=" S1 82U A1301 " pdb=" O2 82U A1301 " ideal model delta sigma weight residual 118.12 100.59 17.53 3.00e+00 1.11e-01 3.42e+01 angle pdb=" CD2 82U B1301 " pdb=" C1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 118.42 101.58 16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C 82U B1302 " pdb=" C1 82U B1302 " pdb=" S1 82U B1302 " ideal model delta sigma weight residual 120.11 136.89 -16.78 3.00e+00 1.11e-01 3.13e+01 ... (remaining 48512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 11118 17.47 - 34.94: 1028 34.94 - 52.41: 262 52.41 - 69.88: 108 69.88 - 87.36: 25 Dihedral angle restraints: 12541 sinusoidal: 6757 harmonic: 5784 Sorted by residual: dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 34.97 58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" C 82U A1301 " pdb=" N 82U A1301 " pdb=" CA 82U A1301 " pdb=" CB 82U A1301 " ideal model delta harmonic sigma weight residual -122.60 -137.94 15.34 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" C 82U B1301 " pdb=" N 82U B1301 " pdb=" CA 82U B1301 " pdb=" CB 82U B1301 " ideal model delta harmonic sigma weight residual -122.60 -137.90 15.30 0 2.50e+00 1.60e-01 3.75e+01 ... (remaining 12538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1387 0.034 - 0.067: 512 0.067 - 0.101: 142 0.101 - 0.134: 49 0.134 - 0.168: 2 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CG LEU B 683 " pdb=" CB LEU B 683 " pdb=" CD1 LEU B 683 " pdb=" CD2 LEU B 683 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA GLN A1149 " pdb=" N GLN A1149 " pdb=" C GLN A1149 " pdb=" CB GLN A1149 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A1086 " pdb=" N ILE A1086 " pdb=" C ILE A1086 " pdb=" CB ILE A1086 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 2089 not shown) Planarity restraints: 3862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 82U B1302 " 0.073 2.00e-02 2.50e+03 8.17e-02 1.67e+02 pdb=" CA 82U B1302 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U B1302 " 0.080 2.00e-02 2.50e+03 pdb=" O 82U B1302 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1302 " 0.070 2.00e-02 2.50e+03 pdb=" CG 82U B1302 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 82U B1302 " -0.000 2.00e-02 2.50e+03 pdb=" C1 82U B1302 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1302 " -0.001 2.00e-02 2.50e+03 pdb=" S1 82U B1302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U B1301 " 0.073 2.00e-02 2.50e+03 8.15e-02 1.66e+02 pdb=" CA 82U B1301 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U B1301 " 0.080 2.00e-02 2.50e+03 pdb=" O 82U B1301 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1301 " 0.068 2.00e-02 2.50e+03 pdb=" CG 82U B1301 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 82U B1301 " -0.000 2.00e-02 2.50e+03 pdb=" C1 82U B1301 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1301 " 0.000 2.00e-02 2.50e+03 pdb=" S1 82U B1301 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U A1301 " 0.072 2.00e-02 2.50e+03 8.13e-02 1.65e+02 pdb=" CA 82U A1301 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U A1301 " 0.079 2.00e-02 2.50e+03 pdb=" O 82U A1301 " 0.006 2.00e-02 2.50e+03 pdb=" CB 82U A1301 " 0.068 2.00e-02 2.50e+03 pdb=" CG 82U A1301 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 82U A1301 " 0.002 2.00e-02 2.50e+03 pdb=" C1 82U A1301 " -0.001 2.00e-02 2.50e+03 pdb=" C17 82U A1301 " 0.002 2.00e-02 2.50e+03 pdb=" S1 82U A1301 " -0.003 2.00e-02 2.50e+03 ... (remaining 3859 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 3942 2.27 - 2.98: 73486 2.98 - 3.70: 99987 3.70 - 4.42: 151365 4.42 - 5.14: 239673 Nonbonded interactions: 568453 Sorted by model distance: nonbonded pdb=" H MET B 303 " pdb=" O4 82U B1302 " model vdw 1.548 2.450 nonbonded pdb=" O ILE B1054 " pdb=" H SER B1084 " model vdw 1.628 2.450 nonbonded pdb=" O TRP B1132 " pdb=" HG SER B1179 " model vdw 1.629 2.450 nonbonded pdb="HD22 ASN B 506 " pdb=" OG SER B 621 " model vdw 1.645 2.450 nonbonded pdb=" O GLN A 591 " pdb=" HG SER A 594 " model vdw 1.655 2.450 ... (remaining 568448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 283 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 284 through 907 or (resi \ d 908 and (name N or name CA or name C or name O or name CB or name CG or name N \ D1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD2 or name HE1 or name HE2)) or resid 909 through 1210 or resid 130 \ 1 through 1302)) selection = (chain 'B' and (resid 283 through 1210 or resid 1302 through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.450 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 57.060 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13424 Z= 0.191 Angle : 0.764 18.480 18211 Z= 0.371 Chirality : 0.039 0.168 2092 Planarity : 0.006 0.082 2256 Dihedral : 14.908 87.355 4836 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1660 helix: 1.17 (0.16), residues: 1017 sheet: -1.66 (0.49), residues: 114 loop : -1.84 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 758 HIS 0.009 0.001 HIS A 398 PHE 0.021 0.001 PHE B 495 TYR 0.022 0.001 TYR A 353 ARG 0.010 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.13155 ( 783) hydrogen bonds : angle 5.71400 ( 2295) SS BOND : bond 0.00420 ( 4) SS BOND : angle 1.08061 ( 8) covalent geometry : bond 0.00411 (13420) covalent geometry : angle 0.76346 (18203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1072 MET cc_start: 0.7696 (tpt) cc_final: 0.7463 (tpt) REVERT: B 1125 LYS cc_start: 0.7395 (tptt) cc_final: 0.7170 (tppt) REVERT: A 429 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 697 SER cc_start: 0.8837 (t) cc_final: 0.8255 (t) REVERT: A 713 MET cc_start: 0.7833 (ttp) cc_final: 0.7334 (ttp) REVERT: A 725 ILE cc_start: 0.8108 (mm) cc_final: 0.7888 (mm) REVERT: A 1072 MET cc_start: 0.7456 (tpt) cc_final: 0.7179 (tpt) REVERT: A 1077 SER cc_start: 0.8855 (m) cc_final: 0.8613 (m) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.5488 time to fit residues: 217.1915 Evaluate side-chains 225 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 839 GLN ** A1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125625 restraints weight = 56284.820| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.35 r_work: 0.3420 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13424 Z= 0.226 Angle : 0.611 12.160 18211 Z= 0.324 Chirality : 0.040 0.129 2092 Planarity : 0.006 0.081 2256 Dihedral : 8.701 87.854 1830 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.78 % Allowed : 7.13 % Favored : 92.09 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1660 helix: 1.29 (0.16), residues: 1009 sheet: -1.94 (0.49), residues: 116 loop : -1.98 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 732 HIS 0.006 0.001 HIS B1159 PHE 0.017 0.001 PHE A1210 TYR 0.013 0.001 TYR A 903 ARG 0.004 0.000 ARG A1151 Details of bonding type rmsd hydrogen bonds : bond 0.05325 ( 783) hydrogen bonds : angle 4.75225 ( 2295) SS BOND : bond 0.00417 ( 4) SS BOND : angle 1.04254 ( 8) covalent geometry : bond 0.00503 (13420) covalent geometry : angle 0.61029 (18203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 222 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 TYR cc_start: 0.7328 (m-80) cc_final: 0.6927 (m-80) REVERT: A 428 MET cc_start: 0.7232 (tpp) cc_final: 0.6972 (tpp) REVERT: A 429 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 697 SER cc_start: 0.8993 (t) cc_final: 0.8482 (t) REVERT: A 713 MET cc_start: 0.8250 (ttp) cc_final: 0.7814 (ttp) REVERT: A 725 ILE cc_start: 0.8248 (mm) cc_final: 0.8027 (mm) outliers start: 11 outliers final: 11 residues processed: 230 average time/residue: 0.5837 time to fit residues: 203.4913 Evaluate side-chains 223 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN B 551 ASN B1204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128070 restraints weight = 55510.917| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.36 r_work: 0.3450 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13424 Z= 0.137 Angle : 0.548 11.419 18211 Z= 0.285 Chirality : 0.039 0.187 2092 Planarity : 0.005 0.081 2256 Dihedral : 8.245 89.290 1830 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.00 % Allowed : 8.84 % Favored : 90.16 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1660 helix: 1.47 (0.16), residues: 1011 sheet: -1.64 (0.50), residues: 108 loop : -1.97 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 732 HIS 0.003 0.001 HIS B1159 PHE 0.014 0.001 PHE B 811 TYR 0.012 0.001 TYR A 353 ARG 0.002 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 783) hydrogen bonds : angle 4.48146 ( 2295) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.16782 ( 8) covalent geometry : bond 0.00292 (13420) covalent geometry : angle 0.54787 (18203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 TYR cc_start: 0.7352 (m-80) cc_final: 0.6827 (m-80) REVERT: B 1072 MET cc_start: 0.7972 (tpt) cc_final: 0.7639 (tpt) REVERT: A 428 MET cc_start: 0.7335 (tpp) cc_final: 0.7096 (tpp) REVERT: A 429 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7442 (tm-30) REVERT: A 697 SER cc_start: 0.8949 (t) cc_final: 0.8444 (t) REVERT: A 713 MET cc_start: 0.8139 (ttp) cc_final: 0.7713 (ttp) REVERT: A 725 ILE cc_start: 0.8227 (mm) cc_final: 0.7997 (mm) outliers start: 14 outliers final: 13 residues processed: 243 average time/residue: 0.6670 time to fit residues: 247.8587 Evaluate side-chains 241 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 228 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 1091 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7516 > 50: distance: 353 - 400: 28.068 distance: 362 - 417: 37.510 distance: 379 - 434: 35.285 distance: 386 - 400: 30.427 distance: 387 - 444: 29.564 distance: 400 - 401: 20.808 distance: 400 - 408: 50.667 distance: 401 - 402: 17.047 distance: 401 - 404: 20.214 distance: 401 - 409: 61.367 distance: 402 - 417: 69.206 distance: 404 - 405: 44.571 distance: 404 - 410: 34.329 distance: 404 - 411: 31.848 distance: 405 - 406: 23.943 distance: 405 - 412: 43.156 distance: 405 - 413: 12.185 distance: 406 - 407: 27.726 distance: 407 - 414: 9.498 distance: 407 - 415: 45.046 distance: 407 - 416: 20.519 distance: 418 - 421: 57.170 distance: 418 - 427: 39.760 distance: 419 - 434: 39.751 distance: 421 - 422: 39.087 distance: 421 - 428: 39.717 distance: 421 - 429: 57.176 distance: 422 - 430: 19.098 distance: 422 - 431: 22.673 distance: 425 - 432: 39.340 distance: 434 - 435: 69.051 distance: 434 - 439: 40.570 distance: 435 - 436: 40.948 distance: 435 - 438: 39.146 distance: 436 - 437: 42.718 distance: 436 - 444: 50.532 distance: 444 - 445: 41.734 distance: 444 - 449: 32.270 distance: 445 - 446: 55.494 distance: 445 - 450: 40.087 distance: 446 - 447: 41.153 distance: 446 - 454: 57.400 distance: 448 - 451: 39.553 distance: 448 - 453: 40.388 distance: 454 - 455: 24.949 distance: 454 - 458: 38.961 distance: 455 - 456: 40.423 distance: 455 - 459: 13.851 distance: 455 - 460: 62.925 distance: 456 - 457: 13.293 distance: 456 - 461: 28.959 distance: 461 - 462: 22.191 distance: 461 - 469: 42.391 distance: 462 - 463: 32.888 distance: 462 - 465: 27.195 distance: 462 - 470: 36.624 distance: 463 - 464: 39.665 distance: 463 - 480: 57.454 distance: 465 - 466: 34.375 distance: 465 - 471: 40.758 distance: 465 - 472: 41.979 distance: 466 - 467: 9.339 distance: 466 - 468: 37.990 distance: 466 - 473: 20.896 distance: 467 - 474: 42.400 distance: 467 - 475: 40.411 distance: 467 - 476: 62.534 distance: 468 - 477: 31.264 distance: 468 - 478: 23.729 distance: 468 - 479: 46.189 distance: 480 - 481: 30.153 distance: 480 - 484: 41.562 distance: 481 - 486: 39.229 distance: 482 - 483: 29.277 distance: 482 - 487: 49.365 distance: 487 - 488: 19.003 distance: 487 - 498: 29.649 distance: 488 - 489: 28.530 distance: 488 - 491: 12.147 distance: 488 - 499: 41.356 distance: 491 - 492: 6.244 distance: 492 - 493: 53.082 distance: 492 - 502: 4.888 distance: 492 - 503: 21.566 distance: 493 - 494: 56.696 distance: 493 - 505: 38.164 distance: 494 - 495: 57.500 distance: 494 - 506: 39.435 distance: 495 - 496: 55.877 distance: 495 - 497: 56.844 distance: 511 - 519: 3.717 distance: 512 - 513: 56.200 distance: 512 - 520: 40.758 distance: 513 - 514: 69.589 distance: 513 - 528: 38.396 distance: 515 - 521: 39.277 distance: 515 - 522: 15.589 distance: 516 - 517: 37.181 distance: 516 - 523: 43.436 distance: 516 - 524: 40.355 distance: 517 - 518: 40.137 distance: 518 - 526: 39.515 distance: 518 - 527: 50.679 distance: 528 - 529: 39.181 distance: 529 - 530: 39.964 distance: 530 - 531: 39.760 distance: 530 - 550: 34.968 distance: 532 - 533: 18.798 distance: 532 - 540: 3.899 distance: 533 - 534: 20.795 distance: 533 - 541: 19.422 distance: 533 - 542: 33.729 distance: 535 - 545: 40.066 distance: 535 - 546: 39.773 distance: 536 - 547: 39.641 distance: 536 - 548: 11.355 distance: 536 - 549: 4.449