Starting phenix.real_space_refine on Mon May 19 10:36:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7h_0356/05_2025/6n7h_0356_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7h_0356/05_2025/6n7h_0356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7h_0356/05_2025/6n7h_0356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7h_0356/05_2025/6n7h_0356.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7h_0356/05_2025/6n7h_0356_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7h_0356/05_2025/6n7h_0356_neut.cif" } resolution = 3.6 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1035 atoms to isotropic. 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 Ca 2 9.91 5 Zn 1 6.06 5 S 88 5.16 5 C 11236 2.51 5 N 2816 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17242 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7807 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 947} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 7708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7708 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 42, 'TRANS': 945} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 154 Unusual residues: {'CLR': 3, 'NAG': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'CLR': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {' CA': 2, ' ZN': 1, 'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 11.11, per 1000 atoms: 0.64 Number of scatterers: 17242 At special positions: 0 Unit cell: (144.82, 93.576, 152.618, 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) Zn 1 29.99 Ca 2 19.99 S 88 16.00 O 3099 8.00 N 2816 7.00 C 11236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 327 " distance=2.01 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 304 " distance=2.03 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=4, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG B1501 " - " ASN B 141 " " NAG B1502 " - " ASN B 312 " " NAG B1503 " - " ASN B 349 " " NAG B1504 " - " ASN B 414 " " NAG B1505 " - " ASN B 875 " " NAG D 1 " - " ASN A1000 " " NAG E 1 " - " ASN B1000 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 140 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 182 " 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 10 sheets defined 57.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 74 through 97 removed outlier: 3.672A pdb=" N TRP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.724A pdb=" N LEU A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.513A pdb=" N LEU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.819A pdb=" N ILE A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.899A pdb=" N ASP A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.519A pdb=" N GLN A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.832A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 410 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 438 through 455 Processing helix chain 'A' and resid 467 through 492 removed outlier: 3.850A pdb=" N GLY A 492 " --> pdb=" O CYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 503 through 524 removed outlier: 3.769A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 544 removed outlier: 4.391A pdb=" N GLY A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 567 through 592 Processing helix chain 'A' and resid 592 through 605 removed outlier: 4.027A pdb=" N ARG A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 746 Proline residue: A 742 - end of helix Processing helix chain 'A' and resid 750 through 771 removed outlier: 3.603A pdb=" N VAL A 763 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.968A pdb=" N ASP A 779 " --> pdb=" O ASP A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 removed outlier: 3.543A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 843 through 864 removed outlier: 3.689A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.616A pdb=" N LYS A 874 " --> pdb=" O ASN A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 888 Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 983 through 1004 removed outlier: 3.648A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1018 Processing helix chain 'A' and resid 1024 through 1046 removed outlier: 3.971A pdb=" N LEU A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A1030 " --> pdb=" O HIS A1026 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1075 removed outlier: 4.165A pdb=" N ILE A1055 " --> pdb=" O TRP A1051 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1106 removed outlier: 3.646A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1122 removed outlier: 3.783A pdb=" N ALA A1115 " --> pdb=" O LYS A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1141 Processing helix chain 'A' and resid 1145 through 1152 removed outlier: 3.917A pdb=" N VAL A1149 " --> pdb=" O PHE A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1178 Proline residue: A1172 - end of helix Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.620A pdb=" N PHE B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 124 through 130 removed outlier: 3.770A pdb=" N LEU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.750A pdb=" N ARG B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS B 146 " --> pdb=" O TYR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 187 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 215 through 221 Processing helix chain 'B' and resid 231 through 242 removed outlier: 6.470A pdb=" N TRP B 236 " --> pdb=" O ASP B 233 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU B 237 " --> pdb=" O CYS B 234 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 238 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 242 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.556A pdb=" N PHE B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 368 through 376 removed outlier: 3.647A pdb=" N PHE B 376 " --> pdb=" O MET B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 409 Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.003A pdb=" N LEU B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 455 Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.621A pdb=" N LEU B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.922A pdb=" N GLY B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 removed outlier: 3.898A pdb=" N LEU B 518 " --> pdb=" O ASP B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.685A pdb=" N CYS B 540 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 542 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 543 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 563 removed outlier: 3.930A pdb=" N ALA B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 591 Processing helix chain 'B' and resid 592 through 605 removed outlier: 4.304A pdb=" N MET B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 745 removed outlier: 4.319A pdb=" N ALA B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Proline residue: B 742 - end of helix Processing helix chain 'B' and resid 746 through 768 removed outlier: 3.914A pdb=" N VAL B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 798 removed outlier: 3.976A pdb=" N LYS B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 828 removed outlier: 3.540A pdb=" N TYR B 820 " --> pdb=" O GLN B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 866 removed outlier: 3.981A pdb=" N TYR B 847 " --> pdb=" O MET B 843 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP B 863 " --> pdb=" O PHE B 859 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU B 864 " --> pdb=" O ASP B 860 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 removed outlier: 4.271A pdb=" N ASN B 875 " --> pdb=" O ASN B 872 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY B 876 " --> pdb=" O TYR B 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 872 through 876' Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 901 through 906 removed outlier: 4.104A pdb=" N LYS B 904 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 905 " --> pdb=" O LEU B 902 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG B 906 " --> pdb=" O THR B 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 901 through 906' Processing helix chain 'B' and resid 918 through 928 removed outlier: 4.682A pdb=" N THR B 924 " --> pdb=" O TYR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1004 removed outlier: 3.642A pdb=" N PHE B 987 " --> pdb=" O ASP B 983 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 988 " --> pdb=" O THR B 984 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B1002 " --> pdb=" O CYS B 998 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B1003 " --> pdb=" O SER B 999 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B1004 " --> pdb=" O ASN B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1016 Processing helix chain 'B' and resid 1018 through 1022 removed outlier: 3.890A pdb=" N TYR B1021 " --> pdb=" O TRP B1018 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B1022 " --> pdb=" O GLU B1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1018 through 1022' Processing helix chain 'B' and resid 1024 through 1046 removed outlier: 4.337A pdb=" N LEU B1030 " --> pdb=" O HIS B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1075 removed outlier: 3.537A pdb=" N GLY B1075 " --> pdb=" O MET B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1106 removed outlier: 4.006A pdb=" N VAL B1083 " --> pdb=" O SER B1079 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B1087 " --> pdb=" O VAL B1083 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS B1099 " --> pdb=" O GLU B1095 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1138 removed outlier: 3.571A pdb=" N VAL B1116 " --> pdb=" O ASN B1112 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA B1124 " --> pdb=" O GLU B1120 " (cutoff:3.500A) Proline residue: B1125 - end of helix Processing helix chain 'B' and resid 1139 through 1143 removed outlier: 3.519A pdb=" N SER B1143 " --> pdb=" O LEU B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1169 removed outlier: 4.494A pdb=" N ILE B1158 " --> pdb=" O ALA B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1177 removed outlier: 3.920A pdb=" N VAL B1173 " --> pdb=" O VAL B1169 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.882A pdb=" N ALA C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.863A pdb=" N GLY C 143 " --> pdb=" O HIS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.514A pdb=" N ARG C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.536A pdb=" N LEU A 360 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 418 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.685A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.529A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 908 through 909 removed outlier: 3.568A pdb=" N ASP A 909 " --> pdb=" O ILE A 913 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AA6, first strand: chain 'B' and resid 360 through 361 removed outlier: 3.629A pdb=" N GLN B 160 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 422 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 772 through 773 removed outlier: 6.432A pdb=" N ARG B 772 " --> pdb=" O LEU B1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 975 through 978 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.206A pdb=" N ILE C 85 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU C 126 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP C 147 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP C 172 " --> pdb=" O SER C 184 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2394 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: 5.53 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3608 1.33 - 1.45: 4098 1.45 - 1.57: 9815 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 17665 Sorted by residual: bond pdb=" C MET C 98 " pdb=" N THR C 99 " ideal model delta sigma weight residual 1.332 1.524 -0.192 1.40e-02 5.10e+03 1.87e+02 bond pdb=" C ARG C 123 " pdb=" N VAL C 124 " ideal model delta sigma weight residual 1.330 1.450 -0.120 1.00e-02 1.00e+04 1.43e+02 bond pdb=" C1 NAG B1501 " pdb=" O5 NAG B1501 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C1 NAG B1504 " pdb=" O5 NAG B1504 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.26e+00 bond pdb=" C PRO A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.94e+00 ... (remaining 17660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 23133 3.03 - 6.05: 733 6.05 - 9.08: 141 9.08 - 12.10: 26 12.10 - 15.13: 6 Bond angle restraints: 24039 Sorted by residual: angle pdb=" C ASP C 83 " pdb=" N ILE C 84 " pdb=" CA ILE C 84 " ideal model delta sigma weight residual 123.10 136.45 -13.35 1.29e+00 6.01e-01 1.07e+02 angle pdb=" O ASP C 83 " pdb=" C ASP C 83 " pdb=" N ILE C 84 " ideal model delta sigma weight residual 122.19 110.99 11.20 1.21e+00 6.83e-01 8.57e+01 angle pdb=" N GLY C 196 " pdb=" CA GLY C 196 " pdb=" C GLY C 196 " ideal model delta sigma weight residual 115.21 126.82 -11.61 1.30e+00 5.92e-01 7.98e+01 angle pdb=" N ALA C 192 " pdb=" CA ALA C 192 " pdb=" C ALA C 192 " ideal model delta sigma weight residual 108.96 122.19 -13.23 1.59e+00 3.96e-01 6.93e+01 angle pdb=" N ALA C 187 " pdb=" CA ALA C 187 " pdb=" C ALA C 187 " ideal model delta sigma weight residual 112.23 121.09 -8.86 1.26e+00 6.30e-01 4.95e+01 ... (remaining 24034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.86: 10321 23.86 - 47.73: 436 47.73 - 71.59: 50 71.59 - 95.46: 23 95.46 - 119.32: 25 Dihedral angle restraints: 10855 sinusoidal: 4589 harmonic: 6266 Sorted by residual: dihedral pdb=" CA ARG B 942 " pdb=" C ARG B 942 " pdb=" N PRO B 943 " pdb=" CA PRO B 943 " ideal model delta harmonic sigma weight residual 180.00 121.33 58.67 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA ALA B 357 " pdb=" C ALA B 357 " pdb=" N HIS B 358 " pdb=" CA HIS B 358 " ideal model delta harmonic sigma weight residual 180.00 125.07 54.93 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLU A 836 " pdb=" C GLU A 836 " pdb=" N ASN A 837 " pdb=" CA ASN A 837 " ideal model delta harmonic sigma weight residual 180.00 -130.59 -49.41 0 5.00e+00 4.00e-02 9.76e+01 ... (remaining 10852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2293 0.089 - 0.178: 422 0.178 - 0.266: 51 0.266 - 0.355: 10 0.355 - 0.444: 4 Chirality restraints: 2780 Sorted by residual: chirality pdb=" C1 NAG B1501 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG B1501 " pdb=" O5 NAG B1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA ALA C 192 " pdb=" N ALA C 192 " pdb=" C ALA C 192 " pdb=" CB ALA C 192 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG A1807 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG A1807 " pdb=" O5 NAG A1807 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 2777 not shown) Planarity restraints: 2996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 83 " 0.032 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C ASP C 83 " -0.099 2.00e-02 2.50e+03 pdb=" O ASP C 83 " 0.033 2.00e-02 2.50e+03 pdb=" N ILE C 84 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 123 " -0.025 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C ARG C 123 " 0.082 2.00e-02 2.50e+03 pdb=" O ARG C 123 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL C 124 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1179 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO A1180 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A1180 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1180 " -0.040 5.00e-02 4.00e+02 ... (remaining 2993 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 152 2.59 - 3.16: 14447 3.16 - 3.74: 26536 3.74 - 4.32: 34992 4.32 - 4.90: 57183 Nonbonded interactions: 133310 Sorted by model distance: nonbonded pdb=" O ALA C 187 " pdb=" N ASN C 189 " model vdw 2.008 3.120 nonbonded pdb=" OD2 ASP C 147 " pdb="ZN ZN C 202 " model vdw 2.125 2.230 nonbonded pdb=" OE1 GLU B 149 " pdb=" NH2 ARG C 28 " model vdw 2.159 3.120 nonbonded pdb=" OD1 ASP C 147 " pdb="ZN ZN C 202 " model vdw 2.225 2.230 nonbonded pdb=" OD2 ASP B 821 " pdb=" OH TYR B1001 " model vdw 2.242 3.040 ... (remaining 133305 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 76 through 458 or (resid 459 through 466 and (name N or na \ me CA or name C or name O or name CB )) or resid 467 through 606 or resid 731 th \ rough 888 or (resid 889 and (name N or name CA or name C or name O or name CB )) \ or resid 890 through 892 or (resid 893 through 905 and (name N or name CA or na \ me C or name O or name CB )) or resid 906 through 953 or (resid 954 through 959 \ and (name N or name CA or name C or name O or name CB )) or resid 960 or (resid \ 961 and (name N or name CA or name C or name O or name CB )) or resid 962 throug \ h 1182 or (resid 1183 and (name N or name CA or name C or name O or name CB )) o \ r resid 1803 through 1807 or resid 1810)) selection = (chain 'B' and (resid 76 through 606 or (resid 731 through 737 and (name N or na \ me CA or name C or name O or name CB )) or resid 738 through 1183 or resid 1501 \ through 1503 or resid 1508)) } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.140 Find NCS groups from input model: 0.850 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 0.011 0.440 17691 Z= 0.615 Angle : 1.333 15.126 24093 Z= 0.676 Chirality : 0.071 0.444 2780 Planarity : 0.009 0.073 2984 Dihedral : 14.944 119.321 6811 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.32 % Favored : 87.12 % Rotamer: Outliers : 1.35 % Allowed : 8.53 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.54 % 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: -4.46 (0.14), residues: 2143 helix: -2.49 (0.11), residues: 1142 sheet: -3.32 (0.40), residues: 115 loop : -3.44 (0.18), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 399 HIS 0.014 0.003 HIS B 358 PHE 0.040 0.004 PHE B1152 TYR 0.033 0.004 TYR A1181 ARG 0.011 0.001 ARG B 945 Details of bonding type rmsd link_NAG-ASN : bond 0.01334 ( 12) link_NAG-ASN : angle 5.37018 ( 36) link_BETA1-4 : bond 0.00549 ( 2) link_BETA1-4 : angle 3.06033 ( 6) hydrogen bonds : bond 0.16146 ( 829) hydrogen bonds : angle 6.84799 ( 2394) metal coordination : bond 0.15262 ( 2) SS BOND : bond 0.00872 ( 6) SS BOND : angle 2.80429 ( 12) covalent geometry : bond 0.00953 (17665) covalent geometry : angle 1.31594 (24039) Misc. bond : bond 0.28808 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 529 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8375 (pp) cc_final: 0.8074 (mt) REVERT: A 131 GLU cc_start: 0.8146 (tt0) cc_final: 0.7795 (tt0) REVERT: A 420 LEU cc_start: 0.7393 (pt) cc_final: 0.5641 (mt) REVERT: A 464 LYS cc_start: 0.7334 (mmtm) cc_final: 0.6721 (ttpt) REVERT: A 501 GLN cc_start: 0.7156 (mt0) cc_final: 0.6817 (tp-100) REVERT: A 550 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8783 (tm) REVERT: A 599 ASP cc_start: 0.7511 (t0) cc_final: 0.7100 (t70) REVERT: A 780 ILE cc_start: 0.8254 (pp) cc_final: 0.8048 (pt) REVERT: A 791 ILE cc_start: 0.9317 (mm) cc_final: 0.9090 (mt) REVERT: A 799 SER cc_start: 0.8475 (p) cc_final: 0.8263 (p) REVERT: A 850 ASP cc_start: 0.8118 (t0) cc_final: 0.7791 (t0) REVERT: A 870 PRO cc_start: 0.6715 (Cg_endo) cc_final: 0.5552 (Cg_exo) REVERT: A 956 MET cc_start: 0.8437 (ptt) cc_final: 0.8178 (ptt) REVERT: A 1013 TYR cc_start: 0.7886 (m-10) cc_final: 0.7593 (m-80) REVERT: A 1052 THR cc_start: 0.8108 (p) cc_final: 0.7889 (t) REVERT: A 1063 MET cc_start: 0.7481 (tpt) cc_final: 0.7200 (ttt) REVERT: A 1073 LEU cc_start: 0.8536 (mt) cc_final: 0.8074 (tp) REVERT: B 82 LYS cc_start: 0.6921 (tptm) cc_final: 0.6515 (mttt) REVERT: B 88 PHE cc_start: 0.5523 (t80) cc_final: 0.4974 (t80) REVERT: B 210 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6078 (pp) REVERT: B 216 MET cc_start: 0.7841 (tpp) cc_final: 0.7373 (tpp) REVERT: B 354 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7426 (pp) REVERT: B 430 ILE cc_start: 0.8488 (tp) cc_final: 0.8258 (pt) REVERT: B 487 LEU cc_start: 0.8198 (tp) cc_final: 0.7759 (tp) REVERT: B 606 ARG cc_start: 0.5980 (mtm180) cc_final: 0.5610 (mtt-85) REVERT: B 744 LEU cc_start: 0.6111 (tt) cc_final: 0.5729 (mt) REVERT: B 760 LEU cc_start: 0.6622 (tt) cc_final: 0.6096 (mm) REVERT: B 868 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5838 (tp) REVERT: B 962 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6650 (tpp80) REVERT: B 1040 PHE cc_start: 0.7792 (t80) cc_final: 0.7517 (t80) REVERT: B 1099 HIS cc_start: 0.7146 (m-70) cc_final: 0.6927 (m-70) REVERT: B 1119 LEU cc_start: 0.7999 (tp) cc_final: 0.7417 (tp) REVERT: C 72 ARG cc_start: 0.6754 (mtp-110) cc_final: 0.6409 (mtp180) REVERT: C 114 MET cc_start: 0.8318 (mtm) cc_final: 0.8098 (mtp) REVERT: C 183 CYS cc_start: 0.7974 (m) cc_final: 0.7743 (m) outliers start: 24 outliers final: 7 residues processed: 545 average time/residue: 0.3035 time to fit residues: 243.0565 Evaluate side-chains 284 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 273 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 188 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.8980 chunk 162 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 124 optimal weight: 0.0270 chunk 194 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 156 GLN A 184 GLN A 310 ASN A 496 ASN A 823 HIS A 871 ASN A 929 ASN A1049 ASN B 120 ASN B 124 ASN B 156 GLN B 201 HIS B 242 GLN B 310 ASN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 846 HIS ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 929 ASN B 938 GLN B1049 ASN C 69 ASN C 107 ASN C 134 HIS C 180 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121218 restraints weight = 29605.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123439 restraints weight = 19123.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124343 restraints weight = 13090.532| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17691 Z= 0.152 Angle : 0.831 15.843 24093 Z= 0.403 Chirality : 0.049 0.292 2780 Planarity : 0.006 0.062 2984 Dihedral : 11.284 72.414 2983 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.89 % Favored : 90.01 % Rotamer: Outliers : 4.04 % Allowed : 14.03 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.29 % 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: -2.71 (0.17), residues: 2143 helix: -0.89 (0.14), residues: 1178 sheet: -2.28 (0.44), residues: 114 loop : -3.01 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1027 HIS 0.012 0.001 HIS B 739 PHE 0.021 0.002 PHE A 848 TYR 0.026 0.002 TYR A 224 ARG 0.008 0.001 ARG B 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 12) link_NAG-ASN : angle 4.05280 ( 36) link_BETA1-4 : bond 0.00386 ( 2) link_BETA1-4 : angle 1.51868 ( 6) hydrogen bonds : bond 0.04625 ( 829) hydrogen bonds : angle 4.95296 ( 2394) metal coordination : bond 0.00913 ( 2) SS BOND : bond 0.01091 ( 6) SS BOND : angle 2.65192 ( 12) covalent geometry : bond 0.00316 (17665) covalent geometry : angle 0.81446 (24039) Misc. bond : bond 0.00141 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6724 (pmm) cc_final: 0.6500 (pmm) REVERT: A 173 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: A 292 MET cc_start: 0.7962 (mmt) cc_final: 0.7591 (mmt) REVERT: A 434 PHE cc_start: 0.7123 (t80) cc_final: 0.6736 (t80) REVERT: A 464 LYS cc_start: 0.7321 (mmtm) cc_final: 0.6668 (ttpt) REVERT: A 862 ASP cc_start: 0.7155 (t70) cc_final: 0.6878 (t0) REVERT: A 1051 TRP cc_start: 0.7003 (t-100) cc_final: 0.6397 (t60) REVERT: A 1073 LEU cc_start: 0.8351 (mt) cc_final: 0.8111 (tp) REVERT: A 1122 MET cc_start: 0.7956 (ttm) cc_final: 0.7585 (ttm) REVERT: A 1175 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8728 (mt) REVERT: B 78 TRP cc_start: 0.6419 (p-90) cc_final: 0.6187 (p-90) REVERT: B 82 LYS cc_start: 0.6992 (tptm) cc_final: 0.6561 (mptt) REVERT: B 101 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5715 (t80) REVERT: B 102 LEU cc_start: 0.5498 (mp) cc_final: 0.5209 (tt) REVERT: B 210 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.5922 (pp) REVERT: B 354 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7416 (pp) REVERT: B 430 ILE cc_start: 0.8329 (tp) cc_final: 0.8062 (pt) REVERT: B 606 ARG cc_start: 0.5970 (mtm180) cc_final: 0.5569 (mtt-85) REVERT: B 740 TYR cc_start: 0.6859 (t80) cc_final: 0.6625 (t80) REVERT: B 760 LEU cc_start: 0.6565 (tt) cc_final: 0.5854 (mm) REVERT: B 868 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.5949 (tp) REVERT: B 962 ARG cc_start: 0.7028 (ttt180) cc_final: 0.6774 (tpp80) REVERT: B 1040 PHE cc_start: 0.7714 (t80) cc_final: 0.7445 (t80) REVERT: B 1111 LYS cc_start: 0.7740 (ttpp) cc_final: 0.7507 (tppt) outliers start: 72 outliers final: 25 residues processed: 377 average time/residue: 0.2689 time to fit residues: 155.2591 Evaluate side-chains 271 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 51.0177 > 50: distance: 4 - 21: 4.721 distance: 8 - 27: 4.705 distance: 12 - 35: 11.389 distance: 16 - 21: 4.135 distance: 17 - 41: 14.587 distance: 22 - 23: 8.993 distance: 22 - 25: 11.708 distance: 23 - 24: 5.754 distance: 23 - 27: 8.271 distance: 24 - 49: 12.202 distance: 25 - 26: 18.039 distance: 27 - 28: 5.049 distance: 28 - 29: 4.612 distance: 28 - 31: 8.806 distance: 29 - 30: 5.877 distance: 29 - 35: 4.385 distance: 30 - 56: 19.724 distance: 31 - 32: 10.270 distance: 31 - 33: 21.947 distance: 32 - 34: 26.899 distance: 35 - 36: 7.909 distance: 36 - 37: 10.272 distance: 36 - 39: 12.601 distance: 37 - 38: 13.278 distance: 37 - 41: 10.982 distance: 38 - 63: 5.516 distance: 39 - 40: 19.521 distance: 41 - 42: 9.466 distance: 42 - 43: 16.833 distance: 43 - 44: 7.984 distance: 43 - 49: 3.767 distance: 44 - 68: 13.649 distance: 45 - 46: 10.720 distance: 46 - 47: 5.646 distance: 46 - 48: 14.877 distance: 49 - 50: 7.616 distance: 50 - 51: 16.695 distance: 50 - 53: 8.196 distance: 51 - 52: 16.369 distance: 51 - 56: 9.487 distance: 52 - 79: 29.508 distance: 53 - 54: 21.901 distance: 53 - 55: 3.544 distance: 56 - 57: 12.718 distance: 57 - 58: 8.632 distance: 58 - 59: 3.149 distance: 58 - 63: 4.327 distance: 59 - 90: 11.807 distance: 60 - 61: 5.781 distance: 60 - 62: 7.952 distance: 63 - 64: 4.327 distance: 64 - 65: 14.768 distance: 64 - 67: 7.967 distance: 65 - 66: 13.201 distance: 65 - 68: 12.233 distance: 66 - 98: 16.941 distance: 68 - 69: 22.854 distance: 69 - 70: 7.927 distance: 69 - 72: 10.128 distance: 70 - 71: 29.959 distance: 70 - 79: 30.366 distance: 72 - 73: 10.572 distance: 73 - 74: 8.510 distance: 73 - 75: 14.093 distance: 74 - 76: 7.274 distance: 75 - 77: 4.364 distance: 76 - 78: 9.720 distance: 77 - 78: 10.490 distance: 79 - 80: 13.829 distance: 80 - 81: 31.279 distance: 80 - 83: 6.655 distance: 81 - 82: 9.818 distance: 81 - 90: 10.038 distance: 83 - 84: 8.081 distance: 84 - 85: 13.047 distance: 84 - 86: 17.394 distance: 85 - 87: 10.714 distance: 86 - 88: 9.071 distance: 87 - 89: 18.337 distance: 88 - 89: 16.533 distance: 90 - 91: 4.755 distance: 92 - 93: 4.821 distance: 92 - 98: 6.960 distance: 94 - 95: 3.796 distance: 95 - 96: 7.301 distance: 96 - 97: 5.435 distance: 166 - 172: 3.030