Starting phenix.real_space_refine on Sat Jun 21 09:45:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n9b_24255/06_2025/7n9b_24255.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n9b_24255/06_2025/7n9b_24255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n9b_24255/06_2025/7n9b_24255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n9b_24255/06_2025/7n9b_24255.map" model { file = "/net/cci-nas-00/data/ceres_data/7n9b_24255/06_2025/7n9b_24255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n9b_24255/06_2025/7n9b_24255.cif" } resolution = 3.8 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 15696 2.51 5 N 4112 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24575 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7631 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 8 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 7560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7560 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7618 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 52, 'TRANS': 935} Chain breaks: 9 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 885 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 16.55, per 1000 atoms: 0.67 Number of scatterers: 24575 At special positions: 0 Unit cell: (136.95, 122.84, 195.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 4661 8.00 N 4112 7.00 C 15696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 617 " distance=2.05 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 580 " distance=2.02 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 682 " distance=2.01 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 741 " distance=2.02 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 841 " distance=2.01 Simple disulfide: pdb=" SG CYS A1124 " - pdb=" SG CYS A1135 " distance=2.00 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 258 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 453 " distance=2.04 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 580 " distance=2.04 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B1124 " - pdb=" SG CYS B1135 " distance=2.00 Simple disulfide: pdb=" SG CYS B1174 " - pdb=" SG CYS B1218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 393 " distance=2.04 Simple disulfide: pdb=" SG CYS C 428 " - pdb=" SG CYS C 453 " distance=2.02 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 524 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 617 " distance=2.02 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 580 " distance=2.00 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 709 " - pdb=" SG CYS C 741 " distance=2.03 Simple disulfide: pdb=" SG CYS C 754 " - pdb=" SG CYS C 763 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 841 " distance=2.02 Simple disulfide: pdb=" SG CYS C1124 " - pdb=" SG CYS C1135 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 94 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 94 " 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: 5.78 Conformation dependent library (CDL) restraints added in 3.2 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 56 sheets defined 24.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 429 through 435 removed outlier: 4.240A pdb=" N VAL A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 456 through 463 removed outlier: 3.792A pdb=" N LEU A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.752A pdb=" N LEU A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASN A 480 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.626A pdb=" N ARG A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 829 through 835 Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.740A pdb=" N LEU A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 875 removed outlier: 3.500A pdb=" N LEU A 855 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 867 " --> pdb=" O ALA A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 917 Processing helix chain 'A' and resid 958 through 976 Processing helix chain 'A' and resid 977 through 980 removed outlier: 4.103A pdb=" N PHE A 980 " --> pdb=" O GLY A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 980' Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.554A pdb=" N ILE A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1011 removed outlier: 3.531A pdb=" N TYR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1033 removed outlier: 3.793A pdb=" N GLN A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A1033 " --> pdb=" O SER A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1057 Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1068 through 1076 removed outlier: 3.746A pdb=" N LEU A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1124 removed outlier: 4.718A pdb=" N VAL A1083 " --> pdb=" O PRO A1079 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A1084 " --> pdb=" O GLU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1239 Processing helix chain 'B' and resid 386 through 396 Processing helix chain 'B' and resid 429 through 435 removed outlier: 4.000A pdb=" N VAL B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.892A pdb=" N ILE B 502 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 530 through 535 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 829 through 836 Processing helix chain 'B' and resid 838 through 846 removed outlier: 3.557A pdb=" N LEU B 846 " --> pdb=" O SER B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 849 No H-bonds generated for 'chain 'B' and resid 847 through 849' Processing helix chain 'B' and resid 852 through 875 removed outlier: 3.587A pdb=" N ASP B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 918 Processing helix chain 'B' and resid 958 through 977 Processing helix chain 'B' and resid 978 through 981 Processing helix chain 'B' and resid 989 through 1002 Processing helix chain 'B' and resid 1004 through 1011 removed outlier: 4.348A pdb=" N LEU B1008 " --> pdb=" O THR B1004 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1033 Processing helix chain 'B' and resid 1037 through 1057 Processing helix chain 'B' and resid 1058 through 1060 No H-bonds generated for 'chain 'B' and resid 1058 through 1060' Processing helix chain 'B' and resid 1068 through 1074 Processing helix chain 'B' and resid 1077 through 1126 removed outlier: 4.415A pdb=" N VAL B1083 " --> pdb=" O PRO B1079 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B1084 " --> pdb=" O GLU B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1232 through 1239 removed outlier: 4.094A pdb=" N GLU B1236 " --> pdb=" O PRO B1232 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B1239 " --> pdb=" O PRO B1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 441 through 445 removed outlier: 3.755A pdb=" N TRP C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 463 removed outlier: 4.059A pdb=" N LEU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing helix chain 'C' and resid 508 through 514 Processing helix chain 'C' and resid 594 through 597 Processing helix chain 'C' and resid 829 through 835 Processing helix chain 'C' and resid 838 through 846 removed outlier: 3.643A pdb=" N LEU C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 850 through 875 removed outlier: 3.595A pdb=" N LEU C 855 " --> pdb=" O PHE C 851 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 856 " --> pdb=" O CYS C 852 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 867 " --> pdb=" O ALA C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 918 removed outlier: 3.572A pdb=" N LEU C 913 " --> pdb=" O PRO C 909 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 918 " --> pdb=" O LEU C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 976 Processing helix chain 'C' and resid 977 through 980 removed outlier: 3.669A pdb=" N PHE C 980 " --> pdb=" O GLY C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 977 through 980' Processing helix chain 'C' and resid 989 through 1002 Processing helix chain 'C' and resid 1005 through 1011 Processing helix chain 'C' and resid 1011 through 1033 removed outlier: 3.769A pdb=" N GLN C1027 " --> pdb=" O ILE C1023 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP C1028 " --> pdb=" O GLY C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1057 Processing helix chain 'C' and resid 1058 through 1060 No H-bonds generated for 'chain 'C' and resid 1058 through 1060' Processing helix chain 'C' and resid 1068 through 1075 Processing helix chain 'C' and resid 1077 through 1125 removed outlier: 4.451A pdb=" N VAL C1083 " --> pdb=" O PRO C1079 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN C1084 " --> pdb=" O GLU C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1232 through 1239 removed outlier: 4.043A pdb=" N GLU C1236 " --> pdb=" O PRO C1232 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'F' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 123 removed outlier: 3.622A pdb=" N THR A 121 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 154 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN A 153 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A 361 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 356 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 358 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 182 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 280 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 319 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER A 297 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 128 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 147 removed outlier: 3.742A pdb=" N ASP A 379 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 removed outlier: 4.110A pdb=" N GLY A 195 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 411 removed outlier: 5.418A pdb=" N ILE A 404 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 691 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN A 406 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 689 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 408 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 686 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 741 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 450 removed outlier: 3.529A pdb=" N TYR A 488 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 448 through 450 removed outlier: 3.529A pdb=" N TYR A 488 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA8, first strand: chain 'A' and resid 544 through 546 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AB1, first strand: chain 'A' and resid 630 through 635 removed outlier: 3.517A pdb=" N GLY A 642 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 635 " --> pdb=" O LEU A 638 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 745 through 747 removed outlier: 5.977A pdb=" N GLU A 746 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR A 788 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 783 " --> pdb=" O GLN A 767 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 793 through 796 removed outlier: 6.784A pdb=" N ALA A 793 " --> pdb=" O ILE C 880 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS C 882 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN A 795 " --> pdb=" O LYS C 882 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 803 through 806 Processing sheet with id=AB5, first strand: chain 'A' and resid 813 through 820 removed outlier: 6.009A pdb=" N TYR A1159 " --> pdb=" O HIS A1140 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N HIS A1140 " --> pdb=" O TYR A1159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 828 Processing sheet with id=AB7, first strand: chain 'A' and resid 879 through 882 removed outlier: 3.701A pdb=" N LYS A 882 " --> pdb=" O ASN B 795 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1212 through 1213 Processing sheet with id=AB9, first strand: chain 'A' and resid 1186 through 1188 Processing sheet with id=AC1, first strand: chain 'B' and resid 120 through 123 removed outlier: 3.858A pdb=" N VAL B 359 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 186 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B 282 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 287 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 295 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 147 removed outlier: 3.531A pdb=" N LEU B 368 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 379 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.625A pdb=" N LEU B 176 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 330 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 210 through 213 Processing sheet with id=AC5, first strand: chain 'B' and resid 403 through 409 removed outlier: 3.533A pdb=" N THR B 691 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 687 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 741 " --> pdb=" O TYR B 704 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY B 740 " --> pdb=" O THR B 737 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 416 through 418 removed outlier: 3.894A pdb=" N GLU B 416 " --> pdb=" O CYS B 630 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 446 through 450 removed outlier: 4.077A pdb=" N ASN B 446 " --> pdb=" O SER B 491 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 491 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 608 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 527 " --> pdb=" O THR B 468 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 468 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 544 through 546 Processing sheet with id=AC9, first strand: chain 'B' and resid 746 through 747 removed outlier: 6.712A pdb=" N ILE B 762 " --> pdb=" O ILE B 758 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 803 through 807 Processing sheet with id=AD2, first strand: chain 'B' and resid 810 through 814 Processing sheet with id=AD3, first strand: chain 'B' and resid 810 through 814 removed outlier: 5.950A pdb=" N TYR B1159 " --> pdb=" O HIS B1140 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N HIS B1140 " --> pdb=" O TYR B1159 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 826 through 828 Processing sheet with id=AD5, first strand: chain 'B' and resid 1212 through 1213 Processing sheet with id=AD6, first strand: chain 'B' and resid 1186 through 1188 Processing sheet with id=AD7, first strand: chain 'C' and resid 120 through 122 removed outlier: 7.909A pdb=" N ASN C 153 " --> pdb=" O TYR C 361 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR C 361 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 188 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN C 280 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 293 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP C 320 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 295 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL C 128 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 147 removed outlier: 3.560A pdb=" N ASP C 145 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 368 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP C 379 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.599A pdb=" N ARG C 329 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AE2, first strand: chain 'C' and resid 403 through 406 removed outlier: 3.752A pdb=" N GLY C 740 " --> pdb=" O THR C 737 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 446 through 450 removed outlier: 3.527A pdb=" N ASN C 446 " --> pdb=" O SER C 491 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 486 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 488 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 490 " --> pdb=" O VAL C 604 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 544 through 546 Processing sheet with id=AE5, first strand: chain 'C' and resid 565 through 566 removed outlier: 3.652A pdb=" N TYR C 581 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 634 through 635 removed outlier: 3.540A pdb=" N PHE C 635 " --> pdb=" O LEU C 638 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 643 through 646 Processing sheet with id=AE8, first strand: chain 'C' and resid 745 through 747 removed outlier: 6.110A pdb=" N GLU C 746 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR C 788 " --> pdb=" O GLU C 746 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 762 " --> pdb=" O ILE C 758 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 803 through 806 Processing sheet with id=AF1, first strand: chain 'C' and resid 810 through 820 removed outlier: 3.557A pdb=" N MET C1142 " --> pdb=" O VAL C1157 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C1159 " --> pdb=" O HIS C1140 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS C1140 " --> pdb=" O TYR C1159 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 825 through 828 removed outlier: 4.468A pdb=" N LYS C 825 " --> pdb=" O LEU C 953 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1212 through 1214 Processing sheet with id=AF4, first strand: chain 'C' and resid 1186 through 1189 Processing sheet with id=AF5, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.665A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 67 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.800A pdb=" N VAL D 12 " --> pdb=" O SER D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.072A pdb=" N ASN D 57 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 48 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE D 45 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG D 36 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 32 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 31 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 91 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.072A pdb=" N ASN D 57 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 48 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE D 45 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG D 36 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 32 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 31 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 91 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 113 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.350A pdb=" N LEU F 20 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 79 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS F 22 " --> pdb=" O ILE F 77 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.687A pdb=" N ALA F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG F 36 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE F 45 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA F 48 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN F 57 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 11 through 13 974 hydrogen bonds defined for protein. 2643 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: 12.42 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4026 1.27 - 1.41: 6435 1.41 - 1.55: 14530 1.55 - 1.68: 0 1.68 - 1.82: 132 Bond restraints: 25123 Sorted by residual: bond pdb=" CD GLU A 576 " pdb=" OE2 GLU A 576 " ideal model delta sigma weight residual 1.249 1.137 0.112 1.90e-02 2.77e+03 3.45e+01 bond pdb=" C PRO A 820 " pdb=" O PRO A 820 " ideal model delta sigma weight residual 1.233 1.170 0.063 1.16e-02 7.43e+03 2.92e+01 bond pdb=" C PRO B1149 " pdb=" O PRO B1149 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.13e-02 7.83e+03 2.91e+01 bond pdb=" CA SER B1113 " pdb=" CB SER B1113 " ideal model delta sigma weight residual 1.528 1.448 0.081 1.59e-02 3.96e+03 2.57e+01 bond pdb=" CA SER A1129 " pdb=" CB SER A1129 " ideal model delta sigma weight residual 1.531 1.454 0.077 1.52e-02 4.33e+03 2.56e+01 ... (remaining 25118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 34075 4.88 - 9.77: 137 9.77 - 14.65: 2 14.65 - 19.53: 0 19.53 - 24.42: 2 Bond angle restraints: 34216 Sorted by residual: angle pdb=" CE2 TYR C 581 " pdb=" CZ TYR C 581 " pdb=" OH TYR C 581 " ideal model delta sigma weight residual 119.90 95.48 24.42 3.00e+00 1.11e-01 6.63e+01 angle pdb=" N THR A 710 " pdb=" CA THR A 710 " pdb=" C THR A 710 " ideal model delta sigma weight residual 113.38 103.52 9.86 1.23e+00 6.61e-01 6.43e+01 angle pdb=" N THR C 710 " pdb=" CA THR C 710 " pdb=" C THR C 710 " ideal model delta sigma weight residual 113.17 103.82 9.35 1.26e+00 6.30e-01 5.51e+01 angle pdb=" N THR F 101 " pdb=" CA THR F 101 " pdb=" C THR F 101 " ideal model delta sigma weight residual 114.04 105.74 8.30 1.24e+00 6.50e-01 4.48e+01 angle pdb=" CE1 TYR C 581 " pdb=" CZ TYR C 581 " pdb=" OH TYR C 581 " ideal model delta sigma weight residual 119.90 139.88 -19.98 3.00e+00 1.11e-01 4.44e+01 ... (remaining 34211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13494 17.88 - 35.75: 1149 35.75 - 53.63: 198 53.63 - 71.50: 33 71.50 - 89.38: 34 Dihedral angle restraints: 14908 sinusoidal: 5642 harmonic: 9266 Sorted by residual: dihedral pdb=" CB CYS A1124 " pdb=" SG CYS A1124 " pdb=" SG CYS A1135 " pdb=" CB CYS A1135 " ideal model delta sinusoidal sigma weight residual -86.00 -170.76 84.76 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS C 754 " pdb=" SG CYS C 754 " pdb=" SG CYS C 763 " pdb=" CB CYS C 763 " ideal model delta sinusoidal sigma weight residual -86.00 -9.88 -76.12 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS C1124 " pdb=" SG CYS C1124 " pdb=" SG CYS C1135 " pdb=" CB CYS C1135 " ideal model delta sinusoidal sigma weight residual -86.00 -158.97 72.97 1 1.00e+01 1.00e-02 6.79e+01 ... (remaining 14905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3187 0.131 - 0.262: 723 0.262 - 0.394: 14 0.394 - 0.525: 1 0.525 - 0.656: 2 Chirality restraints: 3927 Sorted by residual: chirality pdb=" CA CYS C 709 " pdb=" N CYS C 709 " pdb=" C CYS C 709 " pdb=" CB CYS C 709 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" CA CYS A 709 " pdb=" N CYS A 709 " pdb=" C CYS A 709 " pdb=" CB CYS A 709 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 3924 not shown) Planarity restraints: 4433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 581 " -0.057 2.00e-02 2.50e+03 3.98e-02 3.17e+01 pdb=" CG TYR C 581 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 581 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR C 581 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 581 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR C 581 " 0.054 2.00e-02 2.50e+03 pdb=" CZ TYR C 581 " -0.055 2.00e-02 2.50e+03 pdb=" OH TYR C 581 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 45 " -0.014 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE D 45 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE D 45 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE D 45 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE D 45 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE D 45 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 45 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 85 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C LYS D 85 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS D 85 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO D 86 " 0.022 2.00e-02 2.50e+03 ... (remaining 4430 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 470 2.64 - 3.20: 23060 3.20 - 3.77: 36222 3.77 - 4.33: 50626 4.33 - 4.90: 84267 Nonbonded interactions: 194645 Sorted by model distance: nonbonded pdb=" OH TYR A 581 " pdb=" O THR D 101 " model vdw 2.070 3.040 nonbonded pdb=" O THR A 485 " pdb=" OG1 THR A 615 " model vdw 2.203 3.040 nonbonded pdb=" O ASP A 386 " pdb=" OG SER A 389 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR C 129 " pdb=" O LEU C 146 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLN D 1 " pdb=" OH TYR D 106 " model vdw 2.254 3.040 ... (remaining 194640 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 119 through 144 or (resid 145 and (name N or name CA or na \ me C or name O or name CB )) or resid 146 through 158 or resid 174 through 187 o \ r (resid 188 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 89 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 200 or (resid 201 through 205 and (name N or name CA \ or name C or name O or name CB )) or resid 208 through 216 or (resid 217 and (na \ me N or name CA or name C or name O or name CB )) or resid 218 through 223 or (r \ esid 224 and (name N or name CA or name C or name O or name CB )) or resid 225 o \ r (resid 226 through 230 and (name N or name CA or name C or name O or name CB ) \ ) or resid 231 through 232 or resid 259 through 263 or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or resid 278 through 288 or resid 292 \ through 303 or (resid 307 and (name N or name CA or name C or name O or name CB \ )) or resid 308 through 309 or (resid 310 and (name N or name CA or name C or n \ ame O or name CB )) or resid 311 through 315 or (resid 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 330 or (resid 331 and ( \ name N or name CA or name C or name O or name CB )) or resid 332 through 400 or \ (resid 401 and (name N or name CA or name C or name O or name CB )) or resid 402 \ through 424 or (resid 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 477 or (resid 478 and (name N or name CA or name C or n \ ame O or name CB )) or resid 479 through 499 or (resid 500 and (name N or name C \ A or name C or name O or name CB )) or resid 501 through 515 or (resid 516 and ( \ name N or name CA or name C or name O or name CB )) or resid 517 through 520 or \ (resid 521 and (name N or name CA or name C or name O or name CB )) or resid 522 \ through 549 or (resid 550 and (name N or name CA or name C or name O or name CB \ )) or resid 551 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 581 or (resid 582 and (name N or name C \ A or name C or name O or name CB )) or resid 583 through 620 or (resid 621 and ( \ name N or name CA or name C or name O or name CB )) or resid 622 through 645 or \ (resid 646 and (name N or name CA or name C or name O or name CB )) or resid 647 \ through 649 or (resid 650 and (name N or name CA or name C or name O or name CB \ )) or resid 651 or (resid 652 and (name N or name CA or name C or name O or nam \ e CB )) or resid 653 through 669 or (resid 670 and (name N or name CA or name C \ or name O or name CB )) or resid 671 through 885 or (resid 886 and (name N or na \ me CA or name C or name O or name CB )) or resid 887 or (resid 888 and (name N o \ r name CA or name C or name O or name CB )) or resid 889 through 903 or resid 90 \ 5 through 979 or (resid 980 and (name N or name CA or name C or name O or name C \ B )) or resid 981 through 1239)) selection = (chain 'B' and (resid 119 through 158 or resid 174 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 205 o \ r resid 208 through 220 or (resid 221 and (name N or name CA or name C or name O \ or name CB )) or resid 222 through 226 or (resid 227 through 230 and (name N or \ name CA or name C or name O or name CB )) or resid 231 through 232 or resid 259 \ through 279 or (resid 280 and (name N or name CA or name C or name O or name CB \ )) or resid 281 or (resid 282 and (name N or name CA or name C or name O or nam \ e CB )) or resid 283 through 287 or (resid 288 and (name N or name CA or name C \ or name O or name CB )) or resid 292 through 333 or (resid 334 through 356 and ( \ name N or name CA or name C or name O or name CB )) or resid 357 through 372 or \ (resid 373 and (name N or name CA or name C or name O or name CB )) or resid 374 \ through 448 or (resid 449 and (name N or name CA or name C or name O or name CB \ )) or resid 450 through 515 or (resid 516 and (name N or name CA or name C or n \ ame O or name CB )) or resid 517 through 549 or (resid 550 and (name N or name C \ A or name C or name O or name CB )) or resid 551 through 575 or (resid 576 and ( \ name N or name CA or name C or name O or name CB )) or resid 577 through 581 or \ (resid 582 and (name N or name CA or name C or name O or name CB )) or resid 583 \ through 659 or (resid 660 and (name N or name CA or name C or name O or name CB \ )) or resid 661 through 673 or (resid 674 through 675 and (name N or name CA or \ name C or name O or name CB )) or resid 676 through 677 or (resid 678 and (name \ N or name CA or name C or name O or name CB )) or resid 679 through 705 or (res \ id 706 and (name N or name CA or name C or name O or name CB )) or resid 707 thr \ ough 710 or (resid 711 and (name N or name CA or name C or name O or name CB )) \ or resid 712 through 768 or resid 782 through 836 or (resid 837 and (name N or n \ ame CA or name C or name O or name CB )) or resid 838 through 919 or resid 947 t \ hrough 1239)) selection = (chain 'C' and (resid 119 through 144 or (resid 145 and (name N or name CA or na \ me C or name O or name CB )) or resid 146 through 158 or resid 174 through 187 o \ r (resid 188 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 89 through 200 or (resid 201 through 205 and (name N or name CA or name C or nam \ e O or name CB )) or resid 208 through 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 223 or (resid 224 and (na \ me N or name CA or name C or name O or name CB )) or resid 225 or (resid 226 thr \ ough 230 and (name N or name CA or name C or name O or name CB )) or resid 231 t \ hrough 232 or resid 259 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB )) or resid 278 through 281 or (resid 282 and (name N or \ name CA or name C or name O or name CB )) or resid 283 through 288 or resid 292 \ through 303 or (resid 307 and (name N or name CA or name C or name O or name CB \ )) or resid 308 through 309 or (resid 310 and (name N or name CA or name C or n \ ame O or name CB )) or resid 311 through 315 or (resid 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 330 or (resid 331 and ( \ name N or name CA or name C or name O or name CB )) or resid 332 through 400 or \ (resid 401 and (name N or name CA or name C or name O or name CB )) or resid 402 \ through 424 or (resid 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 448 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB )) or resid 450 through 477 or (resid 478 and (name N or name C \ A or name C or name O or name CB )) or resid 479 through 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 520 or \ (resid 521 and (name N or name CA or name C or name O or name CB )) or resid 522 \ through 620 or (resid 621 and (name N or name CA or name C or name O or name CB \ )) or resid 622 through 645 or (resid 646 and (name N or name CA or name C or n \ ame O or name CB )) or resid 647 through 649 or (resid 650 and (name N or name C \ A or name C or name O or name CB )) or resid 651 or (resid 652 and (name N or na \ me CA or name C or name O or name CB )) or resid 653 through 659 or (resid 660 a \ nd (name N or name CA or name C or name O or name CB )) or resid 661 through 669 \ or (resid 670 and (name N or name CA or name C or name O or name CB )) or resid \ 671 through 885 or (resid 886 and (name N or name CA or name C or name O or nam \ e CB )) or resid 887 or (resid 888 and (name N or name CA or name C or name O or \ name CB )) or resid 889 through 979 or (resid 980 and (name N or name CA or nam \ e C or name O or name CB )) or resid 981 through 1239)) } ncs_group { reference = (chain 'D' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 117)) selection = chain 'F' } 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 group one per residue 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: 73.620 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: 0.050 Extract box with map and model: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 61.060 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.110 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.013 0.112 25154 Z= 0.938 Angle : 1.417 24.418 34278 Z= 0.989 Chirality : 0.101 0.656 3927 Planarity : 0.007 0.047 4433 Dihedral : 13.967 89.378 8855 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.41 (0.14), residues: 3133 helix: 1.82 (0.19), residues: 654 sheet: -0.19 (0.19), residues: 686 loop : -1.13 (0.13), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP B 978 HIS 0.008 0.002 HIS B1140 PHE 0.059 0.003 PHE D 45 TYR 0.057 0.004 TYR C 581 ARG 0.036 0.001 ARG F 31 Details of bonding type rmsd hydrogen bonds : bond 0.21670 ( 950) hydrogen bonds : angle 8.72160 ( 2643) SS BOND : bond 0.01351 ( 31) SS BOND : angle 3.39878 ( 62) covalent geometry : bond 0.01344 (25123) covalent geometry : angle 1.41097 (34216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 2.800 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.6869 (m-10) cc_final: 0.6577 (m-80) REVERT: A 560 ILE cc_start: 0.7766 (pt) cc_final: 0.7432 (mt) REVERT: B 1042 ASP cc_start: 0.8145 (t70) cc_final: 0.7674 (t70) REVERT: C 397 SER cc_start: 0.8799 (p) cc_final: 0.8552 (p) REVERT: F 81 MET cc_start: 0.2147 (mpp) cc_final: 0.1784 (mtm) outliers start: 2 outliers final: 2 residues processed: 300 average time/residue: 0.3300 time to fit residues: 161.5573 Evaluate side-chains 242 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 1132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.6980 chunk 239 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 247 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 217 ASN A 452 ASN A 540 ASN A 542 ASN A 993 GLN A1234 GLN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN ** C1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109203 restraints weight = 40388.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110336 restraints weight = 25799.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110244 restraints weight = 18692.499| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25154 Z= 0.148 Angle : 0.633 9.921 34278 Z= 0.338 Chirality : 0.047 0.167 3927 Planarity : 0.005 0.053 4433 Dihedral : 4.872 26.211 3413 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.86 % Allowed : 11.06 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.30 (0.14), residues: 3133 helix: 2.05 (0.20), residues: 654 sheet: -0.29 (0.18), residues: 752 loop : -1.07 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 34 HIS 0.007 0.001 HIS D 30 PHE 0.019 0.001 PHE C 657 TYR 0.023 0.002 TYR C 545 ARG 0.006 0.001 ARG F 31 Details of bonding type rmsd hydrogen bonds : bond 0.05471 ( 950) hydrogen bonds : angle 6.41575 ( 2643) SS BOND : bond 0.00353 ( 31) SS BOND : angle 1.44259 ( 62) covalent geometry : bond 0.00326 (25123) covalent geometry : angle 0.63079 (34216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.7825 (m-80) cc_final: 0.7535 (m-80) REVERT: A 188 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5678 (mm-30) REVERT: B 157 PHE cc_start: 0.7256 (m-10) cc_final: 0.6859 (m-10) REVERT: B 1042 ASP cc_start: 0.7903 (t70) cc_final: 0.7525 (t70) REVERT: C 600 TYR cc_start: 0.8199 (m-80) cc_final: 0.7720 (m-80) REVERT: C 872 GLU cc_start: 0.8014 (tp30) cc_final: 0.7600 (tp30) REVERT: D 19 ARG cc_start: 0.6170 (ttp80) cc_final: 0.5901 (mmt180) REVERT: D 81 MET cc_start: 0.5271 (mtt) cc_final: 0.4596 (ptt) REVERT: F 69 SER cc_start: 0.7547 (t) cc_final: 0.7049 (p) REVERT: F 81 MET cc_start: 0.2390 (mpp) cc_final: 0.1980 (mtm) outliers start: 23 outliers final: 13 residues processed: 304 average time/residue: 0.3351 time to fit residues: 165.2275 Evaluate side-chains 262 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 244 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 310 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 chunk 303 optimal weight: 20.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN A1097 GLN A1166 ASN B 299 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN C1047 ASN C1156 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109081 restraints weight = 40570.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108996 restraints weight = 34403.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109893 restraints weight = 24836.169| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25154 Z= 0.198 Angle : 0.618 9.978 34278 Z= 0.327 Chirality : 0.047 0.315 3927 Planarity : 0.005 0.051 4433 Dihedral : 4.845 30.392 3412 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.09 % Allowed : 13.26 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.49 (0.14), residues: 3133 helix: 1.73 (0.20), residues: 653 sheet: -0.34 (0.19), residues: 700 loop : -1.13 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 34 HIS 0.005 0.001 HIS C 141 PHE 0.021 0.002 PHE A 184 TYR 0.026 0.002 TYR C 545 ARG 0.008 0.001 ARG C 365 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 950) hydrogen bonds : angle 6.04513 ( 2643) SS BOND : bond 0.00439 ( 31) SS BOND : angle 1.65055 ( 62) covalent geometry : bond 0.00468 (25123) covalent geometry : angle 0.61437 (34216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 3.459 Fit side-chains REVERT: A 151 PHE cc_start: 0.7465 (m-80) cc_final: 0.7236 (m-80) REVERT: A 587 TYR cc_start: 0.7167 (m-10) cc_final: 0.6958 (m-10) REVERT: B 157 PHE cc_start: 0.7206 (m-10) cc_final: 0.6879 (m-10) REVERT: B 847 GLN cc_start: 0.8394 (tp40) cc_final: 0.8080 (pt0) REVERT: B 1042 ASP cc_start: 0.7954 (t70) cc_final: 0.7563 (t70) REVERT: C 512 ASP cc_start: 0.6398 (m-30) cc_final: 0.6197 (m-30) REVERT: C 872 GLU cc_start: 0.8026 (tp30) cc_final: 0.7622 (tp30) REVERT: C 915 PHE cc_start: 0.7453 (t80) cc_final: 0.7247 (t80) REVERT: C 1073 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8167 (mp) REVERT: F 69 SER cc_start: 0.7527 (t) cc_final: 0.7039 (p) REVERT: F 81 MET cc_start: 0.2800 (mpp) cc_final: 0.2539 (mtm) outliers start: 56 outliers final: 34 residues processed: 302 average time/residue: 0.3861 time to fit residues: 193.4177 Evaluate side-chains 273 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain B residue 1224 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 1073 LEU Chi-restraints excluded: chain C residue 1109 GLU Chi-restraints excluded: chain C residue 1143 SER Chi-restraints excluded: chain C residue 1196 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 ASN 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: 69.726 > 50: distance: 46 - 53: 31.101 distance: 53 - 54: 10.012 distance: 53 - 182: 33.581 distance: 54 - 55: 57.933 distance: 54 - 57: 30.837 distance: 55 - 56: 46.682 distance: 55 - 62: 17.675 distance: 56 - 179: 24.248 distance: 57 - 58: 11.117 distance: 58 - 59: 19.136 distance: 59 - 60: 19.549 distance: 60 - 61: 9.269 distance: 62 - 63: 10.430 distance: 63 - 64: 37.135 distance: 63 - 66: 46.089 distance: 64 - 65: 35.256 distance: 64 - 68: 25.459 distance: 66 - 67: 45.264 distance: 67 - 178: 27.001 distance: 68 - 69: 55.705 distance: 68 - 172: 30.717 distance: 69 - 70: 47.861 distance: 70 - 71: 26.369 distance: 70 - 80: 43.155 distance: 71 - 169: 32.770 distance: 72 - 73: 50.762 distance: 73 - 74: 16.511 distance: 73 - 75: 7.238 distance: 74 - 76: 18.476 distance: 75 - 77: 39.369 distance: 77 - 78: 49.606 distance: 78 - 79: 39.315 distance: 80 - 81: 49.507 distance: 81 - 82: 6.241 distance: 82 - 83: 54.369 distance: 82 - 84: 59.084 distance: 84 - 85: 37.551 distance: 85 - 86: 11.063 distance: 85 - 88: 44.009 distance: 86 - 87: 48.501 distance: 86 - 91: 31.442 distance: 88 - 89: 41.160 distance: 88 - 90: 10.465 distance: 91 - 92: 13.744 distance: 92 - 93: 44.638 distance: 92 - 95: 18.028 distance: 93 - 94: 42.887 distance: 93 - 97: 31.001 distance: 94 - 111: 32.452 distance: 95 - 96: 21.301 distance: 97 - 98: 31.719 distance: 97 - 103: 54.289 distance: 98 - 99: 19.399 distance: 98 - 101: 21.162 distance: 99 - 100: 12.270 distance: 99 - 104: 41.623 distance: 100 - 120: 9.660 distance: 101 - 102: 39.816 distance: 102 - 103: 42.248 distance: 104 - 105: 22.442 distance: 105 - 106: 39.196 distance: 105 - 108: 11.843 distance: 106 - 107: 56.325 distance: 106 - 111: 36.682 distance: 108 - 109: 39.903 distance: 108 - 110: 41.115 distance: 111 - 112: 38.011 distance: 112 - 113: 53.179 distance: 112 - 115: 52.411 distance: 113 - 114: 54.610 distance: 113 - 120: 52.596 distance: 115 - 116: 31.252 distance: 116 - 117: 10.718 distance: 117 - 118: 42.628 distance: 118 - 119: 44.084 distance: 120 - 121: 40.591 distance: 121 - 122: 52.150 distance: 121 - 124: 56.614 distance: 122 - 123: 22.791 distance: 122 - 128: 31.774 distance: 124 - 125: 55.834 distance: 125 - 126: 39.547 distance: 125 - 127: 33.327