Starting phenix.real_space_refine on Thu Dec 14 13:09:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyd_27075/12_2023/8cyd_27075.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyd_27075/12_2023/8cyd_27075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyd_27075/12_2023/8cyd_27075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyd_27075/12_2023/8cyd_27075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyd_27075/12_2023/8cyd_27075.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyd_27075/12_2023/8cyd_27075.pdb" } resolution = 2.6 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= 0.022 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 129 5.16 5 C 18097 2.51 5 N 4769 2.21 5 O 5459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 773": "OE1" <-> "OE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28454 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8581 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1043} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8585 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8585 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 14.43, per 1000 atoms: 0.51 Number of scatterers: 28454 At special positions: 0 Unit cell: (170.13, 179.76, 200.09, 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 129 16.00 O 5459 8.00 N 4769 7.00 C 18097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.67 Conformation dependent library (CDL) restraints added in 5.0 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 58 sheets defined 22.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.887A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.093A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.757A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 854 removed outlier: 3.504A pdb=" N GLN A 853 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.410A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.265A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.616A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.740A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.157A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.838A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.794A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.699A pdb=" N GLN B 853 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.508A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.500A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.797A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.006A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.625A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 633 through 638 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.790A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.477A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.232A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 4.197A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.811A pdb=" N ILE D 31 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.785A pdb=" N ILE F 31 " --> pdb=" O ASP F 28 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.255A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.835A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.566A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.566A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 154 removed outlier: 7.376A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.736A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 removed outlier: 4.849A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 3.944A pdb=" N ASN A 450 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR A 495 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 452 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN A 493 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.962A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.730A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.023A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.532A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.509A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.293A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.293A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.622A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.850A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.705A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.963A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.305A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 326 through 328 removed outlier: 4.499A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.869A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 448 through 454 removed outlier: 3.991A pdb=" N ASN B 450 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 495 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 452 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN B 493 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.054A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.719A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.049A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.744A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.490A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.387A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.954A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.084A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 153 through 157 removed outlier: 3.587A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.378A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.286A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 448 through 454 removed outlier: 3.940A pdb=" N ASN C 450 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR C 495 " --> pdb=" O ASN C 450 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU C 452 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN C 493 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.101A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 735 through 736 removed outlier: 3.507A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.472A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 3 through 8 Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.170A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER D 120 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL D 12 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.170A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER D 120 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL D 12 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 3 through 8 Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.128A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER E 120 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL E 12 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.128A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER E 120 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL E 12 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.202A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.202A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) 1184 hydrogen bonds defined for protein. 3126 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: 14.52 Time building geometry restraints manager: 12.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9045 1.34 - 1.46: 5204 1.46 - 1.58: 14691 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29105 Sorted by residual: bond pdb=" CE1 HIS C 625 " pdb=" NE2 HIS C 625 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.75e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.456 1.487 -0.031 8.70e-03 1.32e+04 1.28e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.93e+00 bond pdb=" N ILE C 624 " pdb=" CA ILE C 624 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.69e+00 bond pdb=" N LEU A 335 " pdb=" CA LEU A 335 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.37e-02 5.33e+03 8.09e+00 ... (remaining 29100 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.34: 409 104.34 - 111.82: 13926 111.82 - 119.29: 9703 119.29 - 126.76: 15250 126.76 - 134.23: 337 Bond angle restraints: 39625 Sorted by residual: angle pdb=" N PRO C 621 " pdb=" CA PRO C 621 " pdb=" CB PRO C 621 " ideal model delta sigma weight residual 103.25 96.87 6.38 1.05e+00 9.07e-01 3.69e+01 angle pdb=" CA PRO C 621 " pdb=" N PRO C 621 " pdb=" CD PRO C 621 " ideal model delta sigma weight residual 112.00 105.42 6.58 1.40e+00 5.10e-01 2.21e+01 angle pdb=" CA ASN A 334 " pdb=" C ASN A 334 " pdb=" O ASN A 334 " ideal model delta sigma weight residual 122.01 117.46 4.55 1.05e+00 9.07e-01 1.88e+01 angle pdb=" N VAL C 860 " pdb=" CA VAL C 860 " pdb=" C VAL C 860 " ideal model delta sigma weight residual 106.42 112.31 -5.89 1.51e+00 4.39e-01 1.52e+01 angle pdb=" N GLU C 619 " pdb=" CA GLU C 619 " pdb=" C GLU C 619 " ideal model delta sigma weight residual 113.20 108.59 4.61 1.21e+00 6.83e-01 1.45e+01 ... (remaining 39620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16032 17.95 - 35.90: 1066 35.90 - 53.85: 155 53.85 - 71.79: 42 71.79 - 89.74: 24 Dihedral angle restraints: 17319 sinusoidal: 6693 harmonic: 10626 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.64 -89.36 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 174.29 -81.29 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 171.20 -78.20 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 17316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3354 0.039 - 0.079: 721 0.079 - 0.118: 337 0.118 - 0.158: 82 0.158 - 0.197: 3 Chirality restraints: 4497 Sorted by residual: chirality pdb=" CA VAL C 622 " pdb=" N VAL C 622 " pdb=" C VAL C 622 " pdb=" CB VAL C 622 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA VAL C 635 " pdb=" N VAL C 635 " pdb=" C VAL C 635 " pdb=" CB VAL C 635 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CA ILE B 203 " pdb=" N ILE B 203 " pdb=" C ILE B 203 " pdb=" CB ILE B 203 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 4494 not shown) Planarity restraints: 5147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 634 " -1.064 9.50e-02 1.11e+02 4.77e-01 1.37e+02 pdb=" NE ARG C 634 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 634 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 634 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 634 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO C 230 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 862 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO B 863 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 863 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 863 " -0.036 5.00e-02 4.00e+02 ... (remaining 5144 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 192 2.52 - 3.12: 22348 3.12 - 3.71: 43430 3.71 - 4.31: 62738 4.31 - 4.90: 105977 Nonbonded interactions: 234685 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 1.930 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 1.958 2.440 nonbonded pdb=" O ARG C 246 " pdb=" OG1 THR C 250 " model vdw 1.991 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.026 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.051 2.440 ... (remaining 234680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147)) selection = (chain 'C' and (resid 15 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'E' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.020 Extract box with map and model: 14.680 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 79.320 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.190 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:15.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.002 0.042 29105 Z= 0.155 Angle : 0.508 6.732 39625 Z= 0.294 Chirality : 0.043 0.197 4497 Planarity : 0.008 0.477 5147 Dihedral : 12.525 89.743 10389 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.86 % Favored : 94.72 % Rotamer: Outliers : 0.32 % Allowed : 0.22 % Favored : 99.46 % 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: 0.04 (0.14), residues: 3639 helix: 2.08 (0.21), residues: 711 sheet: 0.16 (0.17), residues: 872 loop : -0.78 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.004 0.000 HIS C 146 PHE 0.015 0.001 PHE C 342 TYR 0.021 0.001 TYR B 200 ARG 0.004 0.000 ARG C 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 182 average time/residue: 1.1653 time to fit residues: 259.1455 Evaluate side-chains 122 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 3.237 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 4.4109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 332 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 282 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 625 HIS ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN B1005 GLN C 61 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29105 Z= 0.397 Angle : 0.621 10.945 39625 Z= 0.330 Chirality : 0.048 0.283 4497 Planarity : 0.005 0.152 5147 Dihedral : 4.507 42.762 3942 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.39 % Favored : 94.34 % Rotamer: Outliers : 1.36 % Allowed : 5.72 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.09 % 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: -0.14 (0.14), residues: 3639 helix: 1.88 (0.20), residues: 692 sheet: 0.15 (0.17), residues: 873 loop : -0.90 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 258 HIS 0.005 0.001 HIS A1064 PHE 0.025 0.002 PHE C 906 TYR 0.024 0.002 TYR C1067 ARG 0.010 0.001 ARG C 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 16 residues processed: 164 average time/residue: 1.2173 time to fit residues: 242.9086 Evaluate side-chains 130 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 3.032 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.3976 time to fit residues: 5.5001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 359 optimal weight: 20.0000 chunk 296 optimal weight: 0.0670 chunk 330 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29105 Z= 0.286 Angle : 0.558 9.254 39625 Z= 0.295 Chirality : 0.045 0.198 4497 Planarity : 0.004 0.138 5147 Dihedral : 4.409 40.231 3942 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.40 % Favored : 95.30 % Rotamer: Outliers : 1.36 % Allowed : 8.34 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % 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: -0.13 (0.14), residues: 3639 helix: 2.03 (0.20), residues: 686 sheet: 0.20 (0.17), residues: 874 loop : -0.97 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 258 HIS 0.004 0.001 HIS B 146 PHE 0.023 0.001 PHE B 135 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 157 average time/residue: 1.0713 time to fit residues: 210.9469 Evaluate side-chains 135 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 3.195 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.4225 time to fit residues: 6.9425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 0.5980 chunk 250 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 158 optimal weight: 30.0000 chunk 223 optimal weight: 9.9990 chunk 334 optimal weight: 0.0270 chunk 353 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 316 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29105 Z= 0.252 Angle : 0.545 9.661 39625 Z= 0.287 Chirality : 0.044 0.165 4497 Planarity : 0.004 0.137 5147 Dihedral : 4.386 43.033 3942 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.11 % Favored : 94.64 % Rotamer: Outliers : 1.77 % Allowed : 9.38 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % 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: -0.13 (0.14), residues: 3639 helix: 2.09 (0.20), residues: 687 sheet: 0.21 (0.17), residues: 883 loop : -1.00 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 152 HIS 0.003 0.001 HIS B 625 PHE 0.019 0.001 PHE B 135 TYR 0.020 0.001 TYR A 170 ARG 0.003 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 122 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 23 residues processed: 169 average time/residue: 1.0146 time to fit residues: 218.4060 Evaluate side-chains 141 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 3.067 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.4299 time to fit residues: 5.7973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 263 optimal weight: 50.0000 chunk 145 optimal weight: 0.7980 chunk 301 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 chunk 317 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29105 Z= 0.275 Angle : 0.552 10.561 39625 Z= 0.290 Chirality : 0.044 0.191 4497 Planarity : 0.004 0.134 5147 Dihedral : 4.424 40.749 3942 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.64 % Favored : 95.14 % Rotamer: Outliers : 1.74 % Allowed : 10.67 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % 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: -0.14 (0.14), residues: 3639 helix: 2.02 (0.20), residues: 688 sheet: 0.23 (0.17), residues: 867 loop : -1.00 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS A 146 PHE 0.026 0.001 PHE A 168 TYR 0.021 0.001 TYR C 144 ARG 0.003 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 125 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 32 residues processed: 166 average time/residue: 1.0252 time to fit residues: 216.4678 Evaluate side-chains 149 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 3.111 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 0.3114 time to fit residues: 7.7047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 8.9990 chunk 318 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 354 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29105 Z= 0.194 Angle : 0.530 10.908 39625 Z= 0.278 Chirality : 0.043 0.183 4497 Planarity : 0.004 0.137 5147 Dihedral : 4.304 42.483 3942 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.97 % Favored : 94.81 % Rotamer: Outliers : 1.64 % Allowed : 11.37 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3639 helix: 2.12 (0.20), residues: 689 sheet: 0.34 (0.17), residues: 855 loop : -0.96 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.003 0.000 HIS B 146 PHE 0.024 0.001 PHE B 168 TYR 0.019 0.001 TYR A 170 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 125 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 37 residues processed: 164 average time/residue: 1.0148 time to fit residues: 211.9934 Evaluate side-chains 155 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 3.423 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 31 residues processed: 6 average time/residue: 0.4723 time to fit residues: 8.7282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 258 optimal weight: 40.0000 chunk 200 optimal weight: 0.9980 chunk 298 optimal weight: 0.4980 chunk 197 optimal weight: 1.9990 chunk 352 optimal weight: 20.0000 chunk 220 optimal weight: 30.0000 chunk 215 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29105 Z= 0.240 Angle : 0.537 9.198 39625 Z= 0.281 Chirality : 0.044 0.194 4497 Planarity : 0.004 0.137 5147 Dihedral : 4.306 41.477 3942 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.86 % Favored : 94.92 % Rotamer: Outliers : 1.71 % Allowed : 12.00 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3639 helix: 2.06 (0.20), residues: 696 sheet: 0.43 (0.17), residues: 809 loop : -0.96 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.003 0.001 HIS A 207 PHE 0.030 0.001 PHE A 168 TYR 0.023 0.001 TYR B 160 ARG 0.005 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 128 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 35 residues processed: 170 average time/residue: 0.9595 time to fit residues: 208.5977 Evaluate side-chains 151 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 3.056 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 0.2953 time to fit residues: 5.9278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5679 > 50: distance: 5 - 10: 35.042 distance: 10 - 11: 40.888 distance: 11 - 12: 53.311 distance: 11 - 14: 7.109 distance: 12 - 18: 39.108 distance: 14 - 15: 45.918 distance: 15 - 16: 46.177 distance: 15 - 17: 33.772 distance: 18 - 19: 34.563 distance: 19 - 20: 54.095 distance: 19 - 22: 35.322 distance: 20 - 21: 39.210 distance: 20 - 26: 39.096 distance: 22 - 23: 43.824 distance: 23 - 24: 45.409 distance: 23 - 25: 55.008 distance: 26 - 27: 34.892 distance: 27 - 28: 31.343 distance: 27 - 30: 45.547 distance: 28 - 29: 57.368 distance: 28 - 32: 40.917 distance: 30 - 31: 43.120 distance: 31 - 115: 29.696 distance: 32 - 33: 29.546 distance: 32 - 38: 48.204 distance: 33 - 34: 42.121 distance: 33 - 36: 3.869 distance: 34 - 35: 33.445 distance: 34 - 39: 11.815 distance: 36 - 37: 53.909 distance: 37 - 38: 43.356 distance: 39 - 40: 15.236 distance: 40 - 41: 31.355 distance: 40 - 43: 32.412 distance: 41 - 42: 55.620 distance: 41 - 50: 39.737 distance: 42 - 70: 41.936 distance: 43 - 44: 39.345 distance: 44 - 45: 21.060 distance: 44 - 46: 35.807 distance: 45 - 47: 34.661 distance: 46 - 48: 39.491 distance: 47 - 49: 41.527 distance: 50 - 51: 55.322 distance: 51 - 52: 8.669 distance: 52 - 53: 47.797 distance: 52 - 54: 48.789 distance: 53 - 81: 32.838 distance: 54 - 55: 33.170 distance: 55 - 56: 15.629 distance: 55 - 58: 41.878 distance: 56 - 57: 39.152 distance: 56 - 63: 44.035 distance: 58 - 59: 34.476 distance: 59 - 60: 22.614 distance: 60 - 61: 42.447 distance: 60 - 62: 40.875 distance: 63 - 64: 48.153 distance: 64 - 65: 33.855 distance: 64 - 67: 20.601 distance: 65 - 70: 32.869 distance: 67 - 68: 58.493 distance: 67 - 69: 13.703 distance: 70 - 71: 6.839 distance: 71 - 72: 17.528 distance: 71 - 74: 23.562 distance: 72 - 73: 12.053 distance: 72 - 81: 19.760 distance: 74 - 75: 26.510 distance: 75 - 76: 25.441 distance: 75 - 77: 24.603 distance: 76 - 78: 28.745 distance: 77 - 79: 24.955 distance: 78 - 80: 5.234 distance: 79 - 80: 17.047 distance: 81 - 82: 13.600 distance: 82 - 83: 7.542 distance: 82 - 85: 27.401 distance: 83 - 84: 18.203 distance: 83 - 89: 11.105 distance: 85 - 86: 22.964 distance: 86 - 87: 10.433 distance: 86 - 88: 15.638