Starting phenix.real_space_refine on Mon Dec 11 10:55:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/12_2023/8fez_29035_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/12_2023/8fez_29035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/12_2023/8fez_29035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/12_2023/8fez_29035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/12_2023/8fez_29035_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/12_2023/8fez_29035_neut.pdb" } resolution = 3.72 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= 0.003 sd= 0.034 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 77 5.16 5 C 11056 2.51 5 N 3127 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 905": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17515 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 5931 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 387} Link IDs: {'PTRANS': 48, 'TRANS': 906} Chain breaks: 17 Unresolved non-hydrogen bonds: 1605 Unresolved non-hydrogen angles: 2088 Unresolved non-hydrogen dihedrals: 1279 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'GLN:plan1': 33, 'ARG:plan': 24, 'TYR:plan': 13, 'ASN:plan1': 38, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 35, 'GLU:plan': 32, 'ASP:plan': 32} Unresolved non-hydrogen planarities: 876 Chain: "B" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 5621 Classifications: {'peptide': 916} Incomplete info: {'truncation_to_alanine': 403} Link IDs: {'PTRANS': 43, 'TRANS': 872} Chain breaks: 17 Unresolved non-hydrogen bonds: 1565 Unresolved non-hydrogen angles: 2042 Unresolved non-hydrogen dihedrals: 1201 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 42, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 36, 'TRP:plan': 2, 'ASP:plan': 39, 'PHE:plan': 26, 'GLU:plan': 32, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 816 Chain: "C" Number of atoms: 5963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 5963 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 441} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 14 Unresolved non-hydrogen bonds: 1698 Unresolved non-hydrogen angles: 2218 Unresolved non-hydrogen dihedrals: 1303 Unresolved non-hydrogen chiralities: 232 Planarities with less than four sites: {'GLN:plan1': 41, 'ASP:plan': 38, 'TYR:plan': 16, 'ASN:plan1': 41, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 23, 'GLU:plan': 34, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 880 Time building chain proxies: 10.09, per 1000 atoms: 0.58 Number of scatterers: 17515 At special positions: 0 Unit cell: (131.072, 139.264, 179.2, 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 77 16.00 O 3255 8.00 N 3127 7.00 C 11056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.07 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=1.75 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.24 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.16 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.13 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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: 7.26 Conformation dependent library (CDL) restraints added in 4.2 seconds 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5336 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 40 sheets defined 25.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.572A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.713A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 749 through 756 removed outlier: 3.646A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 882 removed outlier: 4.602A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 910 Processing helix chain 'A' and resid 922 through 936 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.242A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.924A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.023A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.658A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.464A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 882 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.575A pdb=" N PHE B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.561A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 990 removed outlier: 4.372A pdb=" N GLU B 990 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1032 Processing helix chain 'B' and resid 1116 through 1120 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.443A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.643A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.118A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 784 through 786 No H-bonds generated for 'chain 'C' and resid 784 through 786' Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.395A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.736A pdb=" N LEU C 877 " --> pdb=" O TYR C 873 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TRP C 886 " --> pdb=" O ILE C 882 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR C 887 " --> pdb=" O THR C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.668A pdb=" N PHE C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 936 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.986A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 984 through 1033 removed outlier: 5.588A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1120 Processing helix chain 'C' and resid 1125 through 1129 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.528A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.773A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 206 removed outlier: 3.901A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.873A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.458A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AA6, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.567A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 575 through 576 removed outlier: 7.203A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.655A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.232A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.727A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.727A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.815A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.932A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.321A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.376A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.219A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 393 Processing sheet with id=AC3, first strand: chain 'B' and resid 433 through 434 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.897A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AC6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.103A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 888 through 889 Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1096 removed outlier: 4.476A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.928A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.796A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD4, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.559A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.454A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.164A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.034A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.775A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.807A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.955A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.655A 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: 4.410A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1096 815 hydrogen bonds defined for protein. 2190 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: 7.82 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 5006 1.33 - 1.48: 5967 1.48 - 1.64: 6788 1.64 - 1.79: 33 1.79 - 1.95: 45 Bond restraints: 17839 Sorted by residual: bond pdb=" CA ILE C 434 " pdb=" CB ILE C 434 " ideal model delta sigma weight residual 1.541 1.464 0.078 1.28e-02 6.10e+03 3.70e+01 bond pdb=" CA SER A 116 " pdb=" CB SER A 116 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.35e-02 5.49e+03 3.15e+01 bond pdb=" CA LYS C 97 " pdb=" C LYS C 97 " ideal model delta sigma weight residual 1.525 1.451 0.073 1.32e-02 5.74e+03 3.10e+01 bond pdb=" CA HIS A1048 " pdb=" C HIS A1048 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.42e-02 4.96e+03 3.06e+01 bond pdb=" CA GLY A 550 " pdb=" C GLY A 550 " ideal model delta sigma weight residual 1.516 1.451 0.065 1.18e-02 7.18e+03 3.05e+01 ... (remaining 17834 not shown) Histogram of bond angle deviations from ideal: 95.35 - 103.44: 313 103.44 - 111.52: 7082 111.52 - 119.61: 7675 119.61 - 127.69: 9360 127.69 - 135.78: 79 Bond angle restraints: 24509 Sorted by residual: angle pdb=" N HIS C1088 " pdb=" CA HIS C1088 " pdb=" C HIS C1088 " ideal model delta sigma weight residual 108.78 119.10 -10.32 8.20e-01 1.49e+00 1.59e+02 angle pdb=" N ILE A 410 " pdb=" CA ILE A 410 " pdb=" C ILE A 410 " ideal model delta sigma weight residual 110.36 98.30 12.06 1.05e+00 9.07e-01 1.32e+02 angle pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" C ASN A 99 " ideal model delta sigma weight residual 114.56 102.05 12.51 1.27e+00 6.20e-01 9.70e+01 angle pdb=" N VAL B1122 " pdb=" CA VAL B1122 " pdb=" C VAL B1122 " ideal model delta sigma weight residual 112.17 120.73 -8.56 9.50e-01 1.11e+00 8.11e+01 angle pdb=" N PHE C 374 " pdb=" CA PHE C 374 " pdb=" C PHE C 374 " ideal model delta sigma weight residual 110.24 97.62 12.62 1.41e+00 5.03e-01 8.02e+01 ... (remaining 24504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 10127 18.08 - 36.16: 251 36.16 - 54.23: 74 54.23 - 72.31: 14 72.31 - 90.39: 7 Dihedral angle restraints: 10473 sinusoidal: 2272 harmonic: 8201 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -176.39 90.39 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 -176.92 -90.08 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 3.48 -89.48 1 1.00e+01 1.00e-02 9.51e+01 ... (remaining 10470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2334 0.121 - 0.241: 481 0.241 - 0.362: 70 0.362 - 0.483: 19 0.483 - 0.603: 3 Chirality restraints: 2907 Sorted by residual: chirality pdb=" CA ASN B1074 " pdb=" N ASN B1074 " pdb=" C ASN B1074 " pdb=" CB ASN B1074 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" CG LEU A 117 " pdb=" CB LEU A 117 " pdb=" CD1 LEU A 117 " pdb=" CD2 LEU A 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" CA VAL A 511 " pdb=" N VAL A 511 " pdb=" C VAL A 511 " pdb=" CB VAL A 511 " both_signs ideal model delta sigma weight residual False 2.44 2.96 -0.52 2.00e-01 2.50e+01 6.77e+00 ... (remaining 2904 not shown) Planarity restraints: 3337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 612 " -0.146 2.00e-02 2.50e+03 9.11e-02 1.66e+02 pdb=" CG TYR A 612 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 612 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 612 " 0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR A 612 " 0.081 2.00e-02 2.50e+03 pdb=" CE2 TYR A 612 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR A 612 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 612 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 37 " 0.084 2.00e-02 2.50e+03 4.57e-02 4.17e+01 pdb=" CG TYR A 37 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 37 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR A 37 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 37 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 37 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 37 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 37 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 756 " -0.076 2.00e-02 2.50e+03 3.98e-02 3.16e+01 pdb=" CG TYR A 756 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 756 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 756 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 756 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 756 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 756 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 756 " -0.054 2.00e-02 2.50e+03 ... (remaining 3334 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 9 2.33 - 2.97: 10377 2.97 - 3.62: 25476 3.62 - 4.26: 36364 4.26 - 4.90: 58008 Nonbonded interactions: 130234 Sorted by model distance: nonbonded pdb=" NZ LYS A 195 " pdb=" CB ILE A 203 " model vdw 1.688 3.550 nonbonded pdb=" O ASP B 574 " pdb=" OD1 ASP B 574 " model vdw 2.110 3.040 nonbonded pdb=" OG SER A 94 " pdb=" O ALA A 264 " model vdw 2.207 2.440 nonbonded pdb=" O LYS A 825 " pdb=" CG1 VAL A 826 " model vdw 2.223 3.460 nonbonded pdb=" OD1 ASN A 501 " pdb=" N GLY A 502 " model vdw 2.235 2.520 ... (remaining 130229 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' and ((resid 29 through 31 and (name N or name CA or name C or name O \ or name CB )) or (resid 32 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1)) or (resid 33 and (name N or name CA or name C or name \ O or name CB )) or resid 34 through 43 or (resid 44 through 46 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 through 49 or (resid 50 thro \ ugh 56 and (name N or name CA or name C or name O or name CB )) or resid 57 thro \ ugh 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or \ resid 61 or (resid 62 through 64 and (name N or name CA or name C or name O or n \ ame CB )) or resid 65 through 67 or (resid 68 and (name N or name CA or name C o \ r name O or name CB )) or resid 69 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 85 or (resid 86 through 88 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 89 through 96 and (na \ me N or name CA or name C or name O or name CB )) or (resid 99 through 106 and ( \ name N or name CA or name C or name O or name CB )) or (resid 107 through 113 an \ d (name N or name CA or name C or name O or name CB )) or (resid 117 through 121 \ and (name N or name CA or name C or name O or name CB )) or resid 122 through 1 \ 23 or (resid 124 through 130 and (name N or name CA or name C or name O or name \ CB )) or (resid 135 and (name N or name CA or name C or name O or name CB )) or \ (resid 137 through 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 through 140 or (resid 141 and (name N or name CA or name C or name \ O or name CB )) or resid 142 through 143 or (resid 164 through 165 and (name N o \ r name CA or name C or name O or name CB )) or resid 166 or (resid 167 and (name \ N or name CA or name C or name O or name CB )) or resid 168 through 171 or (res \ id 172 through 173 and (name N or name CA or name C or name O or name CB )) or r \ esid 174 or (resid 189 through 198 and (name N or name CA or name C or name O or \ name CB )) or resid 199 through 209 or (resid 210 and (name N or name CA or nam \ e C or name O or name CB )) or resid 211 or (resid 215 through 216 and (name N o \ r name CA or name C or name O or name CB )) or resid 217 through 219 or (resid 2 \ 20 through 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 or (resid 226 through 229 and (name N or name CA or name C or name O or nam \ e CB )) or resid 230 through 240 or (resid 265 through 267 and (name N or name C \ A or name C or name O or name CB )) or resid 268 through 269 or (resid 270 throu \ gh 271 and (name N or name CA or name C or name O or name CB )) or resid 272 thr \ ough 273 or (resid 274 through 278 and (name N or name CA or name C or name O or \ name CB )) or resid 279 or (resid 280 through 281 and (name N or name CA or nam \ e C or name O or name CB )) or resid 282 through 284 or (resid 285 through 290 a \ nd (name N or name CA or name C or name O or name CB )) or resid 291 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 or (resid 309 through 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 through 313 or (resid 314 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 315 through 318 or (resid 319 and (n \ ame N or name CA or name C or name O or name CB or name CG )) or (resid 320 thro \ ugh 321 and (name N or name CA or name C or name O or name CB )) or resid 322 or \ (resid 323 through 324 and (name N or name CA or name C or name O or name CB )) \ or resid 325 through 326 or (resid 327 through 329 and (name N or name CA or na \ me C or name O or name CB )) or resid 330 through 331 or (resid 332 and (name N \ or name CA or name C or name O or name CB )) or resid 336 through 337 or (resid \ 338 and (name N or name CA or name C or name O or name CB )) or (resid 339 throu \ gh 342 and (name N or name CA or name C or name O or name CB )) or resid 343 thr \ ough 346 or (resid 352 through 354 and (name N or name CA or name C or name O or \ name CB )) or resid 355 through 361 or (resid 362 through 364 and (name N or na \ me CA or name C or name O or name CB )) or (resid 365 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1)) or (resid 366 through 373 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 376 through 37 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 379 or (resi \ d 380 and (name N or name CA or name C or name O or name CB )) or resid 381 or ( \ resid 382 through 383 and (name N or name CA or name C or name O or name CB )) o \ r resid 384 through 387 or (resid 388 and (name N or name CA or name C or name O \ or name CB or name CG )) or resid 389 through 392 or (resid 393 through 395 and \ (name N or name CA or name C or name O or name CB )) or (resid 405 through 408 \ and (name N or name CA or name C or name O or name CB )) or resid 412 through 41 \ 3 or (resid 414 through 415 and (name N or name CA or name C or name O or name C \ B )) or resid 416 through 422 or (resid 427 through 430 and (name N or name CA o \ r name C or name O or name CB )) or resid 431 through 432 or (resid 433 through \ 439 and (name N or name CA or name C or name O or name CB )) or resid 496 or (re \ sid 503 through 515 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 527 or (resid 528 through 537 and (name N or name CA or name C \ or name O or name CB )) or resid 538 through 539 or (resid 540 through 544 and \ (name N or name CA or name C or name O or name CB )) or resid 545 through 546 or \ (resid 547 and (name N or name CA or name C or name O or name CB )) or resid 54 \ 8 or (resid 549 and (name N or name CA or name C or name O or name CB )) or resi \ d 550 or (resid 551 through 560 and (name N or name CA or name C or name O or na \ me CB )) or resid 561 or (resid 562 and (name N or name CA or name C or name O o \ r name CB )) or (resid 563 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 564 through 568 or (resid 569 through 572 and (name N or \ name CA or name C or name O or name CB )) or resid 573 through 575 or (resid 57 \ 6 through 578 and (name N or name CA or name C or name O or name CB )) or resid \ 579 through 581 or (resid 582 through 588 and (name N or name CA or name C or na \ me O or name CB )) or resid 589 through 596 or (resid 597 through 599 and (name \ N or name CA or name C or name O or name CB )) or resid 600 through 601 or (resi \ d 602 and (name N or name CA or name C or name O or name CB or name CG2)) or res \ id 603 or (resid 604 through 605 and (name N or name CA or name C or name O or n \ ame CB )) or resid 606 or (resid 607 through 611 and (name N or name CA or name \ C or name O or name CB )) or resid 612 or (resid 613 through 615 and (name N or \ name CA or name C or name O or name CB )) or resid 616 through 618 or (resid 619 \ through 620 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 21 through 622 or resid 641 through 644 or (resid 645 through 647 and (name N or \ name CA or name C or name O or name CB )) or resid 648 through 655 or (resid 65 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 657 through \ 658 or (resid 659 and (name N or name CA or name C or name O or name CB )) or re \ sid 660 through 669 or (resid 670 and (name N or name CA or name C or name O or \ name CB )) or resid 671 through 672 or (resid 673 and (name N or name CA or name \ C or name O or name CB )) or resid 674 through 675 or (resid 690 through 695 an \ d (name N or name CA or name C or name O or name CB )) or resid 696 through 698 \ or (resid 699 and (name N or name CA or name C or name O or name CB )) or (resid \ 700 through 708 and (name N or name CA or name C or name O or name CB )) or res \ id 709 or (resid 710 through 714 and (name N or name CA or name C or name O or n \ ame CB )) or resid 715 through 719 or (resid 720 through 721 and (name N or name \ CA or name C or name O or name CB )) or resid 722 through 724 or (resid 725 thr \ ough 726 and (name N or name CA or name C or name O or name CB )) or resid 727 t \ hrough 729 or (resid 730 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 731 and (name N or name CA or name C or name O or name CB or name CG \ )) or resid 732 or (resid 733 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or (resid 734 and (name N or name CA or name C or name O or n \ ame CB )) or resid 735 through 741 or (resid 742 and (name N or name CA or name \ C or name O or name CB )) or resid 743 through 749 or (resid 750 through 751 and \ (name N or name CA or name C or name O or name CB )) or resid 752 through 754 o \ r (resid 755 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 56 through 760 or (resid 761 through 764 and (name N or name CA or name C or nam \ e O or name CB )) or resid 765 through 766 or (resid 767 and (name N or name CA \ or name C or name O or name CB or name CG )) or (resid 768 and (name N or name C \ A or name C or name O or name CB )) or resid 769 or (resid 770 through 778 and ( \ name N or name CA or name C or name O or name CB )) or resid 779 through 781 or \ (resid 782 and (name N or name CA or name C or name O or name CB or name CG )) o \ r (resid 783 through 791 and (name N or name CA or name C or name O or name CB ) \ ) or resid 792 through 793 or (resid 794 through 797 and (name N or name CA or n \ ame C or name O or name CB )) or resid 798 through 801 or (resid 802 and (name N \ or name CA or name C or name O or name CB or name CG )) or (resid 803 through 8 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 807 through \ 809 or (resid 810 through 811 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 812 through 815 and (name N or name CA or name C or name O or \ name CB or name CG or name CD )) or resid 816 through 817 or (resid 818 through \ 821 and (name N or name CA or name C or name O or name CB )) or (resid 822 and ( \ name N or name CA or name C or name O or name CB or name CG )) or (resid 823 thr \ ough 826 and (name N or name CA or name C or name O or name CB )) or resid 853 t \ hrough 855 or (resid 856 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 857 through 861 and (name N or name CA or name C or name O or name C \ B )) or resid 862 through 863 or (resid 864 and (name N or name CA or name C or \ name O or name CB )) or resid 865 or (resid 866 through 872 and (name N or name \ CA or name C or name O or name CB )) or resid 873 through 876 or (resid 877 thro \ ugh 879 and (name N or name CA or name C or name O or name CB )) or (resid 880 t \ hrough 884 and (name N or name CA or name C or name O or name CB )) or resid 885 \ or (resid 886 through 888 and (name N or name CA or name C or name O or name CB \ )) or (resid 889 through 896 and (name N or name CA or name C or name O or name \ CB )) or resid 897 through 898 or (resid 899 through 900 and (name N or name CA \ or name C or name O or name CB )) or (resid 901 through 902 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 903 through 905 or (re \ sid 906 and (name N or name CA or name C or name O or name CB or name CG )) or ( \ resid 907 and (name N or name CA or name C or name O or name CB )) or resid 908 \ or (resid 909 and (name N or name CA or name C or name O or name CB )) or resid \ 910 through 917 or (resid 918 through 925 and (name N or name CA or name C or na \ me O or name CB )) or resid 926 through 930 or (resid 931 and (name N or name CA \ or name C or name O or name CB )) or (resid 932 through 945 and (name N or name \ CA or name C or name O or name CB )) or resid 946 or (resid 947 and (name N or \ name CA or name C or name O or name CB or name CG )) or (resid 948 through 952 a \ nd (name N or name CA or name C or name O or name CB )) or resid 953 or (resid 9 \ 54 through 961 and (name N or name CA or name C or name O or name CB )) or resid \ 962 through 963 or (resid 964 through 969 and (name N or name CA or name C or n \ ame O or name CB )) or resid 970 through 974 or (resid 975 through 977 and (name \ N or name CA or name C or name O or name CB )) or (resid 978 and (name N or nam \ e CA or name C or name O or name CB or name CG )) or (resid 979 through 982 and \ (name N or name CA or name C or name O or name CB )) or resid 983 through 991 or \ (resid 992 through 996 and (name N or name CA or name C or name O or name CB )) \ or resid 997 or (resid 998 and (name N or name CA or name C or name O or name C \ B )) or resid 999 or (resid 1000 through 1006 and (name N or name CA or name C o \ r name O or name CB )) or resid 1007 through 1008 or (resid 1009 and (name N or \ name CA or name C or name O or name CB )) or (resid 1010 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or (resid 1011 through 1 \ 012 and (name N or name CA or name C or name O or name CB or name CG )) or (resi \ d 1013 and (name N or name CA or name C or name O or name CB )) or resid 1014 th \ rough 1018 or (resid 1019 and (name N or name CA or name C or name O or name CB \ or name CG or name CD )) or resid 1020 through 1023 or (resid 1024 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 1025 through 102 \ 7 or (resid 1028 and (name N or name CA or name C or name O or name CB or name C \ G or name CD )) or (resid 1029 through 1031 and (name N or name CA or name C or \ name O or name CB )) or resid 1032 or (resid 1033 through 1034 and (name N or na \ me CA or name C or name O or name CB )) or resid 1035 or (resid 1036 and (name N \ or name CA or name C or name O or name CB or name CG )) or (resid 1037 through \ 1038 and (name N or name CA or name C or name O or name CB )) or (resid 1039 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or r \ esid 1040 through 1048 or (resid 1049 and (name N or name CA or name C or name O \ or name CB )) or resid 1050 through 1053 or (resid 1054 through 1056 and (name \ N or name CA or name C or name O or name CB )) or resid 1057 through 1062 or (re \ sid 1063 and (name N or name CA or name C or name O or name CB )) or resid 1064 \ through 1066 or (resid 1067 and (name N or name CA or name C or name O or name C \ B or name CG )) or (resid 1068 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1069 through 1070 or (resid 1071 through 1073 and (name N or na \ me CA or name C or name O or name CB )) or (resid 1074 through 1075 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 1076 through 10 \ 80 or (resid 1081 and (name N or name CA or name C or name O or name CB )) or re \ sid 1082 through 1083 or (resid 1084 and (name N or name CA or name C or name O \ or name CB )) or resid 1085 through 1087 or (resid 1088 and (name N or name CA o \ r name C or name O or name CB or name CG )) or (resid 1089 and (name N or name C \ A or name C or name O or name CB )) or resid 1090 through 1093 or (resid 1094 th \ rough 1097 and (name N or name CA or name C or name O or name CB )) or resid 109 \ 8 through 1100 or (resid 1101 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 1102 or (resid 1103 through 1106 and (name N or name \ CA or name C or name O or name CB )) or (resid 1107 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 1108 through 1110 or (resid 111 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1112 or (res \ id 1113 through 1120 and (name N or name CA or name C or name O or name CB )) or \ resid 1121 or (resid 1122 through 1123 and (name N or name CA or name C or name \ O or name CB )) or resid 1124 through 1128 or (resid 1129 and (name N or name C \ A or name C or name O or name CB )) or (resid 1130 and (name N or name CA or nam \ e C or name O or name CB or name CG2)) or (resid 1131 through 1133 and (name N o \ r name CA or name C or name O or name CB )) or resid 1134 or (resid 1135 and (na \ me N or name CA or name C or name O or name CB or name CG )) or resid 1136 or (r \ esid 1137 through 1139 and (name N or name CA or name C or name O or name CB )) \ or resid 1140 through 1141 or (resid 1142 through 1143 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'B' and (resid 29 through 50 or (resid 51 through 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 58 or (resid 59 through \ 60 and (name N or name CA or name C or name O or name CB )) or resid 61 through \ 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or res \ id 65 or (resid 66 through 68 and (name N or name CA or name C or name O or name \ CB )) or resid 69 or resid 81 through 82 or (resid 83 through 84 and (name N or \ name CA or name C or name O or name CB )) or resid 85 or (resid 86 through 88 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 89 through 102 \ and (name N or name CA or name C or name O or name CB )) or resid 103 or (resid \ 104 through 106 and (name N or name CA or name C or name O or name CB )) or res \ id 107 or (resid 110 through 113 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 117 through 121 and (name N or name CA or name C or name O o \ r name CB )) or resid 122 through 123 or (resid 124 through 130 and (name N or n \ ame CA or name C or name O or name CB )) or resid 135 or (resid 137 through 138 \ and (name N or name CA or name C or name O or name CB )) or resid 139 through 14 \ 3 or (resid 164 through 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 169 or (resid 170 and (name N or name CA or name C or \ name O or name CB )) or resid 171 through 172 or (resid 173 and (name N or name \ CA or name C or name O or name CB )) or resid 174 or (resid 176 through 198 and \ (name N or name CA or name C or name O or name CB )) or (resid 199 through 203 a \ nd (name N or name CA or name C or name O or name CB )) or resid 204 through 205 \ or (resid 206 through 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 through 210 or (resid 211 and (name N or name CA or name C or n \ ame O or name CB or name CG )) or resid 215 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 or (resid 220 throug \ h 224 and (name N or name CA or name C or name O or name CB )) or resid 225 thro \ ugh 228 or (resid 229 and (name N or name CA or name C or name O or name CB )) o \ r resid 230 through 232 or (resid 233 and (name N or name CA or name C or name O \ or name CB )) or resid 234 through 236 or (resid 237 through 240 and (name N or \ name CA or name C or name O or name CB )) or (resid 265 through 267 and (name N \ or name CA or name C or name O or name CB )) or resid 268 through 272 or (resid \ 273 through 278 and (name N or name CA or name C or name O or name CB )) or res \ id 279 through 285 or (resid 286 through 290 and (name N or name CA or name C or \ name O or name CB )) or resid 291 through 295 or (resid 296 through 300 and (na \ me N or name CA or name C or name O or name CB )) or resid 301 through 305 or (r \ esid 306 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 307 through 316 or (resid 317 through 318 and (name N or name CA or name C \ or name O or name CB )) or (resid 319 and (name N or name CA or name C or name \ O or name CB or name CG )) or (resid 320 through 321 and (name N or name CA or n \ ame C or name O or name CB )) or resid 322 through 328 or (resid 329 and (name N \ or name CA or name C or name O or name CB )) or resid 330 or (resid 331 through \ 332 and (name N or name CA or name C or name O or name CB )) or resid 336 throu \ gh 340 or (resid 341 through 342 and (name N or name CA or name C or name O or n \ ame CB )) or resid 343 through 345 or (resid 346 through 354 and (name N or name \ CA or name C or name O or name CB )) or resid 355 through 356 or (resid 357 thr \ ough 360 and (name N or name CA or name C or name O or name CB )) or resid 361 o \ r (resid 362 through 364 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 365 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1)) or (resid 366 through 378 and (name N or name CA or name C or nam \ e O or name CB )) or resid 379 through 381 or (resid 382 through 383 and (name N \ or name CA or name C or name O or name CB )) or resid 384 through 385 or (resid \ 386 through 387 and (name N or name CA or name C or name O or name CB )) or (re \ sid 388 and (name N or name CA or name C or name O or name CB or name CG )) or r \ esid 389 through 392 or (resid 393 through 408 and (name N or name CA or name C \ or name O or name CB )) or resid 412 through 421 or (resid 422 through 430 and ( \ name N or name CA or name C or name O or name CB )) or resid 431 through 436 or \ (resid 437 through 439 and (name N or name CA or name C or name O or name CB )) \ or resid 496 or (resid 510 through 524 and (name N or name CA or name C or name \ O or name CB )) or resid 525 through 531 or (resid 532 through 537 and (name N o \ r name CA or name C or name O or name CB )) or resid 538 or (resid 539 through 5 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 545 or (res \ id 546 and (name N or name CA or name C or name O or name CB or name CG )) or (r \ esid 547 through 560 and (name N or name CA or name C or name O or name CB )) or \ resid 561 or (resid 562 and (name N or name CA or name C or name O or name CB ) \ ) or resid 563 through 566 or (resid 567 and (name N or name CA or name C or nam \ e O or name CB or name CG )) or (resid 568 through 572 and (name N or name CA or \ name C or name O or name CB )) or resid 573 or (resid 574 through 578 and (name \ N or name CA or name C or name O or name CB )) or resid 579 through 581 or (res \ id 582 through 588 and (name N or name CA or name C or name O or name CB )) or r \ esid 589 through 591 or (resid 592 and (name N or name CA or name C or name O or \ name CB or name CG )) or resid 593 through 594 or (resid 595 through 599 and (n \ ame N or name CA or name C or name O or name CB )) or resid 600 through 603 or ( \ resid 604 through 605 and (name N or name CA or name C or name O or name CB )) o \ r (resid 606 and (name N or name CA or name C or name O or name CB or name CG )) \ or (resid 607 through 611 and (name N or name CA or name C or name O or name CB \ )) or resid 612 through 622 or (resid 641 and (name N or name CA or name C or n \ ame O or name CB )) or resid 642 or (resid 643 through 647 and (name N or name C \ A or name C or name O or name CB )) or resid 648 through 653 or (resid 654 and ( \ name N or name CA or name C or name O or name CB )) or resid 655 or (resid 656 a \ nd (name N or name CA or name C or name O or name CB )) or resid 657 or (resid 6 \ 58 through 659 and (name N or name CA or name C or name O or name CB )) or resid \ 660 through 663 or (resid 664 and (name N or name CA or name C or name O or nam \ e CB )) or resid 665 or (resid 666 and (name N or name CA or name C or name O or \ name CB or name CG2)) or (resid 667 through 670 and (name N or name CA or name \ C or name O or name CB )) or resid 671 through 673 or (resid 674 and (name N or \ name CA or name C or name O or name CB or name CG )) or (resid 675 and (name N o \ r name CA or name C or name O or name CB )) or (resid 690 through 695 and (name \ N or name CA or name C or name O or name CB )) or resid 696 through 698 or (resi \ d 699 and (name N or name CA or name C or name O or name CB )) or (resid 700 thr \ ough 708 and (name N or name CA or name C or name O or name CB )) or resid 709 o \ r (resid 710 through 714 and (name N or name CA or name C or name O or name CB ) \ ) or resid 715 through 717 or (resid 718 and (name N or name CA or name C or nam \ e O or name CB or name CG )) or (resid 719 through 721 and (name N or name CA or \ name C or name O or name CB )) or resid 722 through 725 or (resid 726 and (name \ N or name CA or name C or name O or name CB )) or resid 727 through 729 or (res \ id 730 and (name N or name CA or name C or name O or name CB )) or resid 731 or \ (resid 732 and (name N or name CA or name C or name O or name CB )) or (resid 73 \ 3 and (name N or name CA or name C or name O or name CB or name CG )) or resid 7 \ 34 through 735 or (resid 736 through 737 and (name N or name CA or name C or nam \ e O or name CB )) or resid 738 through 745 or (resid 746 through 748 and (name N \ or name CA or name C or name O or name CB )) or resid 749 or (resid 750 through \ 751 and (name N or name CA or name C or name O or name CB )) or (resid 752 and \ (name N or name CA or name C or name O or name CB or name CG )) or (resid 753 th \ rough 755 and (name N or name CA or name C or name O or name CB )) or resid 756 \ through 757 or (resid 758 and (name N or name CA or name C or name O or name CB \ )) or (resid 759 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 760 through 761 or (resid 762 through 764 and (name N or name CA o \ r name C or name O or name CB )) or resid 765 through 769 or (resid 770 through \ 778 and (name N or name CA or name C or name O or name CB )) or (resid 779 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD )) or res \ id 780 through 786 or (resid 787 through 791 and (name N or name CA or name C or \ name O or name CB )) or resid 792 through 793 or (resid 794 through 797 and (na \ me N or name CA or name C or name O or name CB )) or resid 798 through 802 or (r \ esid 803 through 806 and (name N or name CA or name C or name O or name CB )) or \ resid 807 through 812 or (resid 813 through 814 and (name N or name CA or name \ C or name O or name CB )) or resid 815 through 817 or (resid 818 through 821 and \ (name N or name CA or name C or name O or name CB )) or resid 822 through 825 o \ r (resid 826 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 53 through 857 or (resid 858 through 861 and (name N or name CA or name C or nam \ e O or name CB )) or resid 862 through 866 or (resid 867 through 872 and (name N \ or name CA or name C or name O or name CB )) or resid 873 through 877 or (resid \ 878 through 879 and (name N or name CA or name C or name O or name CB )) or (re \ sid 880 through 884 and (name N or name CA or name C or name O or name CB )) or \ (resid 885 through 888 and (name N or name CA or name C or name O or name CB )) \ or resid 889 through 899 or (resid 900 and (name N or name CA or name C or name \ O or name CB )) or (resid 901 through 902 and (name N or name CA or name C or na \ me O or name CB or name CG )) or resid 903 through 910 or (resid 911 through 915 \ and (name N or name CA or name C or name O or name CB )) or resid 916 through 9 \ 18 or (resid 919 through 925 and (name N or name CA or name C or name O or name \ CB )) or resid 926 through 928 or (resid 929 through 931 and (name N or name CA \ or name C or name O or name CB )) or resid 932 or (resid 933 through 945 and (na \ me N or name CA or name C or name O or name CB )) or resid 946 through 947 or (r \ esid 948 through 952 and (name N or name CA or name C or name O or name CB )) or \ resid 953 through 955 or (resid 956 through 961 and (name N or name CA or name \ C or name O or name CB )) or resid 962 through 964 or (resid 965 through 969 and \ (name N or name CA or name C or name O or name CB )) or resid 970 through 972 o \ r (resid 973 through 977 and (name N or name CA or name C or name O or name CB ) \ ) or resid 978 through 979 or (resid 980 through 982 and (name N or name CA or n \ ame C or name O or name CB )) or resid 983 or (resid 984 through 985 and (name N \ or name CA or name C or name O or name CB )) or resid 986 through 992 or (resid \ 993 through 996 and (name N or name CA or name C or name O or name CB )) or res \ id 997 through 1004 or (resid 1005 through 1006 and (name N or name CA or name C \ or name O or name CB )) or resid 1007 through 1010 or (resid 1011 through 1012 \ and (name N or name CA or name C or name O or name CB or name CG )) or resid 101 \ 3 or (resid 1014 and (name N or name CA or name C or name O or name CB or name C \ G or name CD )) or resid 1015 through 1022 or (resid 1023 and (name N or name CA \ or name C or name O or name CB )) or resid 1024 through 1032 or (resid 1033 thr \ ough 1034 and (name N or name CA or name C or name O or name CB )) or resid 1035 \ through 1038 or (resid 1039 and (name N or name CA or name C or name O or name \ CB or name CG or name CD )) or resid 1040 through 1044 or (resid 1045 and (name \ N or name CA or name C or name O or name CB )) or resid 1046 through 1057 or (re \ sid 1058 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 1059 through 1062 or (resid 1063 and (name N or name CA or name C or name \ O or name CB )) or resid 1064 through 1066 or (resid 1067 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 1068 through 1070 or (res \ id 1071 through 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1076 or (resid 1077 through 1078 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1079 through 1082 or (resid 1083 through \ 1084 and (name N or name CA or name C or name O or name CB )) or resid 1085 thro \ ugh 1087 or (resid 1088 and (name N or name CA or name C or name O or name CB or \ name CG )) or (resid 1089 and (name N or name CA or name C or name O or name CB \ )) or resid 1090 or (resid 1091 and (name N or name CA or name C or name O or n \ ame CB or name CG )) or (resid 1092 through 1097 and (name N or name CA or name \ C or name O or name CB )) or resid 1098 through 1105 or (resid 1106 and (name N \ or name CA or name C or name O or name CB )) or (resid 1107 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 1108 or (resid 1109 and \ (name N or name CA or name C or name O or name CB or name CG )) or (resid 1110 \ through 1111 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 112 through 1113 or (resid 1114 through 1120 and (name N or name CA or name C or \ name O or name CB )) or (resid 1121 and (name N or name CA or name C or name O \ or name CB or name CG )) or (resid 1122 through 1125 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1126 through 1127 or (resid 1128 through \ 1129 and (name N or name CA or name C or name O or name CB )) or resid 1130 thro \ ugh 1131 or (resid 1132 through 1133 and (name N or name CA or name C or name O \ or name CB )) or resid 1134 through 1136 or (resid 1137 through 1139 and (name N \ or name CA or name C or name O or name CB )) or resid 1140 or (resid 1141 throu \ gh 1143 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 29 through 31 and (name N or name CA or name C or name O \ or name CB )) or (resid 32 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1)) or resid 33 or (resid 34 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE )) or resid 35 through \ 43 or (resid 44 through 46 and (name N or name CA or name C or name O or name C \ B )) or resid 47 or (resid 48 and (name N or name CA or name C or name O or name \ CB )) or resid 49 through 54 or (resid 55 through 56 and (name N or name CA or \ name C or name O or name CB )) or resid 57 through 58 or (resid 59 through 60 an \ d (name N or name CA or name C or name O or name CB )) or resid 61 or (resid 62 \ through 64 and (name N or name CA or name C or name O or name CB )) or resid 65 \ through 67 or (resid 68 and (name N or name CA or name C or name O or name CB )) \ or resid 69 or resid 81 through 82 or (resid 83 through 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 90 or (resid 91 through \ 96 and (name N or name CA or name C or name O or name CB )) or (resid 99 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 or ( \ resid 104 through 106 and (name N or name CA or name C or name O or name CB )) o \ r resid 107 or (resid 110 through 121 and (name N or name CA or name C or name O \ or name CB )) or resid 122 through 124 or (resid 125 through 130 and (name N or \ name CA or name C or name O or name CB )) or resid 133 or (resid 137 through 13 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 139 through \ 143 or resid 164 through 169 or (resid 170 and (name N or name CA or name C or n \ ame O or name CB )) or resid 171 through 172 or (resid 173 and (name N or name C \ A or name C or name O or name CB )) or resid 174 or (resid 189 through 198 and ( \ name N or name CA or name C or name O or name CB )) or resid 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ or (resid 205 through 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 through 210 or (resid 211 and (name N or name CA or name C or n \ ame O or name CB or name CG )) or (resid 215 through 216 and (name N or name CA \ or name C or name O or name CB )) or resid 217 through 220 or (resid 221 through \ 224 and (name N or name CA or name C or name O or name CB )) or resid 225 throu \ gh 227 or (resid 228 through 229 and (name N or name CA or name C or name O or n \ ame CB )) or resid 230 through 232 or (resid 233 and (name N or name CA or name \ C or name O or name CB )) or resid 234 through 236 or (resid 237 through 240 and \ (name N or name CA or name C or name O or name CB )) or (resid 265 through 267 \ and (name N or name CA or name C or name O or name CB )) or resid 268 through 26 \ 9 or (resid 270 through 271 and (name N or name CA or name C or name O or name C \ B )) or resid 272 or (resid 273 through 278 and (name N or name CA or name C or \ name O or name CB )) or resid 279 or (resid 280 through 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 283 or (resid 284 thro \ ugh 290 and (name N or name CA or name C or name O or name CB )) or resid 291 th \ rough 292 or (resid 293 through 294 and (name N or name CA or name C or name O o \ r name CB )) or resid 295 or (resid 296 through 300 and (name N or name CA or na \ me C or name O or name CB )) or resid 301 or (resid 302 through 303 and (name N \ or name CA or name C or name O or name CB )) or resid 304 or (resid 305 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 306 and (name N or na \ me CA or name C or name O or name CB or name CG )) or resid 307 through 309 or ( \ resid 310 and (name N or name CA or name C or name O or name CB )) or resid 311 \ or (resid 312 and (name N or name CA or name C or name O or name CB or name CG2) \ ) or resid 313 or (resid 314 and (name N or name CA or name C or name O or name \ CB or name CG )) or (resid 315 through 318 and (name N or name CA or name C or n \ ame O or name CB )) or resid 319 or (resid 320 through 321 and (name N or name C \ A or name C or name O or name CB )) or resid 322 through 325 or (resid 326 throu \ gh 329 and (name N or name CA or name C or name O or name CB )) or resid 330 or \ (resid 331 through 332 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 341 or (resid 342 and (name N or name CA or name C or name \ O or name CB )) or resid 343 through 344 or (resid 345 through 346 and (name N o \ r name CA or name C or name O or name CB )) or (resid 352 through 354 and (name \ N or name CA or name C or name O or name CB )) or resid 355 or (resid 356 throug \ h 360 and (name N or name CA or name C or name O or name CB )) or resid 361 thro \ ugh 373 or (resid 376 through 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 or (resid 380 and (name N or name CA or name C or name O \ or name CB )) or resid 381 through 385 or (resid 386 through 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 through 395 or (resid 40 \ 5 through 408 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 417 or (resid 418 through 422 and (name N or name CA or name C or na \ me O or name CB )) or (resid 427 through 430 and (name N or name CA or name C or \ name O or name CB )) or resid 431 through 439 or resid 504 or (resid 510 throug \ h 515 and (name N or name CA or name C or name O or name CB )) or resid 523 thro \ ugh 527 or (resid 528 through 537 and (name N or name CA or name C or name O or \ name CB )) or resid 538 through 540 or (resid 541 through 544 and (name N or nam \ e CA or name C or name O or name CB )) or resid 545 through 546 or (resid 547 an \ d (name N or name CA or name C or name O or name CB )) or (resid 548 through 560 \ and (name N or name CA or name C or name O or name CB )) or resid 561 through 5 \ 62 or (resid 563 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 564 through 566 or (resid 567 and (name N or name CA or name C or \ name O or name CB or name CG )) or (resid 568 through 572 and (name N or name CA \ or name C or name O or name CB )) or resid 573 or (resid 574 through 578 and (n \ ame N or name CA or name C or name O or name CB )) or resid 579 through 580 or ( \ resid 581 through 588 and (name N or name CA or name C or name O or name CB )) o \ r resid 589 through 590 or (resid 591 and (name N or name CA or name C or name O \ or name CB )) or (resid 592 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 593 through 594 or (resid 595 through 599 and (name N \ or name CA or name C or name O or name CB )) or resid 600 through 601 or (resid \ 602 and (name N or name CA or name C or name O or name CB or name CG2)) or resid \ 603 through 605 or (resid 606 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or (resid 607 through 611 and (name N or name CA or name C or \ name O or name CB )) or resid 612 through 617 or (resid 618 through 620 and (na \ me N or name CA or name C or name O or name CB )) or resid 621 through 622 or (r \ esid 641 and (name N or name CA or name C or name O or name CB )) or resid 642 o \ r (resid 643 through 647 and (name N or name CA or name C or name O or name CB ) \ ) or resid 648 through 649 or (resid 650 through 651 and (name N or name CA or n \ ame C or name O or name CB )) or resid 652 through 657 or (resid 658 through 659 \ and (name N or name CA or name C or name O or name CB )) or resid 660 through 6 \ 63 or (resid 664 and (name N or name CA or name C or name O or name CB )) or res \ id 665 or (resid 666 and (name N or name CA or name C or name O or name CB or na \ me CG2)) or resid 667 through 672 or (resid 673 and (name N or name CA or name C \ or name O or name CB )) or (resid 674 and (name N or name CA or name C or name \ O or name CB or name CG )) or resid 675 or (resid 690 through 695 and (name N or \ name CA or name C or name O or name CB )) or resid 696 through 697 or (resid 69 \ 8 through 699 and (name N or name CA or name C or name O or name CB )) or (resid \ 700 through 708 and (name N or name CA or name C or name O or name CB )) or res \ id 709 through 717 or (resid 718 and (name N or name CA or name C or name O or n \ ame CB or name CG )) or resid 719 through 725 or (resid 726 and (name N or name \ CA or name C or name O or name CB )) or (resid 727 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 728 through 731 or (resid 732 an \ d (name N or name CA or name C or name O or name CB )) or resid 733 through 735 \ or (resid 736 through 737 and (name N or name CA or name C or name O or name CB \ )) or resid 738 or (resid 739 through 740 and (name N or name CA or name C or na \ me O or name CB )) or resid 741 through 746 or (resid 747 through 748 and (name \ N or name CA or name C or name O or name CB )) or resid 749 through 750 or (resi \ d 751 and (name N or name CA or name C or name O or name CB )) or (resid 752 and \ (name N or name CA or name C or name O or name CB or name CG )) or (resid 753 t \ hrough 755 and (name N or name CA or name C or name O or name CB )) or resid 756 \ through 760 or (resid 761 through 764 and (name N or name CA or name C or name \ O or name CB )) or resid 765 through 766 or (resid 767 and (name N or name CA or \ name C or name O or name CB or name CG )) or (resid 768 and (name N or name CA \ or name C or name O or name CB )) or (resid 769 through 778 and (name N or name \ CA or name C or name O or name CB )) or (resid 779 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 780 through 781 or (r \ esid 782 and (name N or name CA or name C or name O or name CB or name CG )) or \ (resid 783 through 791 and (name N or name CA or name C or name O or name CB )) \ or resid 792 through 795 or (resid 796 through 797 and (name N or name CA or nam \ e C or name O or name CB )) or resid 798 through 801 or (resid 802 and (name N o \ r name CA or name C or name O or name CB or name CG )) or (resid 803 through 806 \ and (name N or name CA or name C or name O or name CB )) or resid 807 or (resid \ 808 and (name N or name CA or name C or name O or name CB )) or resid 809 throu \ gh 812 or (resid 813 through 814 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 815 and (name N or name CA or name C or name O or name CB or \ name CG or name CD )) or resid 816 through 822 or (resid 823 through 826 and (n \ ame N or name CA or name C or name O or name CB )) or resid 853 or (resid 854 an \ d (name N or name CA or name C or name O or name CB )) or resid 855 or (resid 85 \ 6 and (name N or name CA or name C or name O or name CB )) or (resid 857 through \ 861 and (name N or name CA or name C or name O or name CB )) or resid 862 throu \ gh 863 or (resid 864 and (name N or name CA or name C or name O or name CB )) or \ resid 865 through 877 or (resid 878 through 879 and (name N or name CA or name \ C or name O or name CB )) or (resid 880 through 884 and (name N or name CA or na \ me C or name O or name CB )) or (resid 885 through 888 and (name N or name CA or \ name C or name O or name CB )) or (resid 889 through 896 and (name N or name CA \ or name C or name O or name CB )) or resid 897 through 898 or (resid 899 throug \ h 900 and (name N or name CA or name C or name O or name CB )) or resid 901 thro \ ugh 905 or (resid 906 and (name N or name CA or name C or name O or name CB or n \ ame CG )) or (resid 907 through 909 and (name N or name CA or name C or name O o \ r name CB )) or (resid 910 through 915 and (name N or name CA or name C or name \ O or name CB )) or resid 916 through 920 or (resid 921 through 925 and (name N o \ r name CA or name C or name O or name CB )) or resid 926 through 930 or (resid 9 \ 31 and (name N or name CA or name C or name O or name CB )) or (resid 932 throug \ h 945 and (name N or name CA or name C or name O or name CB )) or resid 946 or ( \ resid 947 and (name N or name CA or name C or name O or name CB or name CG )) or \ (resid 948 through 952 and (name N or name CA or name C or name O or name CB )) \ or resid 953 through 956 or (resid 957 through 961 and (name N or name CA or na \ me C or name O or name CB )) or resid 962 through 964 or (resid 965 through 969 \ and (name N or name CA or name C or name O or name CB )) or resid 970 through 97 \ 4 or (resid 975 through 977 and (name N or name CA or name C or name O or name C \ B )) or (resid 978 and (name N or name CA or name C or name O or name CB or name \ CG )) or resid 979 through 1003 or (resid 1004 through 1006 and (name N or name \ CA or name C or name O or name CB )) or resid 1007 through 1009 or (resid 1010 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 1011 through 1012 or (resid 1013 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1014 through 1022 or (resid 1023 and (name N or name \ CA or name C or name O or name CB )) or (resid 1024 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 1025 through 1027 or (resid 102 \ 8 and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 1029 through 1037 or (resid 1038 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1039 through 1044 or (resid 1045 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1046 through 1053 or (resid 1054 \ through 1056 and (name N or name CA or name C or name O or name CB )) or resid \ 1057 or (resid 1058 and (name N or name CA or name C or name O or name CB or nam \ e CG )) or resid 1059 through 1073 or (resid 1074 through 1075 and (name N or na \ me CA or name C or name O or name CB or name CG )) or resid 1076 through 1082 or \ (resid 1083 through 1084 and (name N or name CA or name C or name O or name CB \ )) or resid 1085 or (resid 1086 through 1087 and (name N or name CA or name C or \ name O or name CB )) or resid 1088 through 1090 or (resid 1091 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or (resid 1092 and (name N o \ r name CA or name C or name O or name CB )) or (resid 1093 through 1097 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1098 through 1099 or ( \ resid 1100 and (name N or name CA or name C or name O or name CB )) or (resid 11 \ 01 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 1102 or (resid 1103 through 1106 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 1107 through 1109 and (name N or name CA or name C or name O \ or name CB or name CG )) or (resid 1110 through 1111 and (name N or name CA or \ name C or name O or name CB )) or resid 1112 or (resid 1113 through 1120 and (na \ me N or name CA or name C or name O or name CB )) or resid 1121 or (resid 1122 t \ hrough 1123 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 24 through 1129 or (resid 1130 and (name N or name CA or name C or name O or nam \ e CB or name CG2)) or resid 1131 through 1143)) } 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: 0.970 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: 0.010 Extract box with map and model: 4.500 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 53.400 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.018 0.137 17839 Z= 1.245 Angle : 1.765 13.287 24509 Z= 1.212 Chirality : 0.104 0.603 2907 Planarity : 0.010 0.092 3337 Dihedral : 9.254 89.541 5038 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.22 % Allowed : 2.94 % Favored : 96.84 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 2741 helix: -0.30 (0.19), residues: 610 sheet: -0.18 (0.24), residues: 427 loop : -1.22 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.006 TRP A 917 HIS 0.014 0.002 HIS A1088 PHE 0.048 0.006 PHE C 464 TYR 0.154 0.008 TYR A 612 ARG 0.021 0.002 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 369 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 371 average time/residue: 0.2510 time to fit residues: 147.7737 Evaluate side-chains 317 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1747 time to fit residues: 2.7818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 0.8980 chunk 214 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 655 HIS A1010 GLN A1113 GLN B 49 HIS B 422 ASN B 690 GLN B1098 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17839 Z= 0.267 Angle : 0.670 11.158 24509 Z= 0.383 Chirality : 0.047 0.201 2907 Planarity : 0.005 0.063 3337 Dihedral : 5.516 24.198 2886 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 2.94 % Allowed : 10.57 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 2741 helix: 0.49 (0.21), residues: 621 sheet: -0.33 (0.23), residues: 446 loop : -1.56 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.015 0.002 HIS A1088 PHE 0.030 0.002 PHE A1052 TYR 0.033 0.002 TYR B 660 ARG 0.004 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 339 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 353 average time/residue: 0.2535 time to fit residues: 142.5750 Evaluate side-chains 332 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 315 time to evaluate : 1.900 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1611 time to fit residues: 7.7870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 0.1980 chunk 213 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 ASN B 61 ASN B 690 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1058 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17839 Z= 0.313 Angle : 0.675 12.771 24509 Z= 0.384 Chirality : 0.048 0.226 2907 Planarity : 0.005 0.082 3337 Dihedral : 5.629 24.188 2886 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.22 % Favored : 92.74 % Rotamer: Outliers : 3.05 % Allowed : 12.85 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 2741 helix: 0.15 (0.21), residues: 599 sheet: -0.82 (0.22), residues: 478 loop : -1.89 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.016 0.003 HIS B 655 PHE 0.027 0.002 PHE B 92 TYR 0.024 0.002 TYR A 612 ARG 0.009 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 370 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 382 average time/residue: 0.2488 time to fit residues: 152.5508 Evaluate side-chains 362 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 345 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1605 time to fit residues: 7.8332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 254 optimal weight: 0.6980 chunk 193 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 949 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17839 Z= 0.259 Angle : 0.600 8.811 24509 Z= 0.334 Chirality : 0.046 0.165 2907 Planarity : 0.004 0.056 3337 Dihedral : 5.286 24.701 2886 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.75 % Favored : 93.21 % Rotamer: Outliers : 1.96 % Allowed : 17.65 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.15), residues: 2741 helix: 0.41 (0.21), residues: 599 sheet: -0.84 (0.22), residues: 470 loop : -1.90 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.019 0.002 HIS C 49 PHE 0.022 0.002 PHE B 565 TYR 0.025 0.002 TYR A 741 ARG 0.007 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 372 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 379 average time/residue: 0.2483 time to fit residues: 150.5856 Evaluate side-chains 371 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 358 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1577 time to fit residues: 6.4624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 227 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 3 optimal weight: 0.0050 chunk 203 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 ASN B 779 GLN B 787 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17839 Z= 0.204 Angle : 0.560 7.914 24509 Z= 0.309 Chirality : 0.045 0.158 2907 Planarity : 0.004 0.049 3337 Dihedral : 5.017 23.142 2886 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.78 % Rotamer: Outliers : 1.74 % Allowed : 18.95 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2741 helix: 0.60 (0.22), residues: 601 sheet: -0.89 (0.22), residues: 477 loop : -1.87 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 917 HIS 0.009 0.001 HIS C1064 PHE 0.021 0.002 PHE B 43 TYR 0.025 0.002 TYR A1007 ARG 0.006 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 360 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 366 average time/residue: 0.2702 time to fit residues: 160.3983 Evaluate side-chains 368 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 355 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1573 time to fit residues: 6.4654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 54 optimal weight: 0.0670 chunk 160 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 22 optimal weight: 0.0010 chunk 90 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 overall best weight: 2.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17839 Z= 0.317 Angle : 0.650 11.873 24509 Z= 0.364 Chirality : 0.047 0.154 2907 Planarity : 0.005 0.056 3337 Dihedral : 5.545 24.965 2886 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.38 % Favored : 90.55 % Rotamer: Outliers : 3.05 % Allowed : 18.63 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.15), residues: 2741 helix: 0.14 (0.21), residues: 619 sheet: -0.95 (0.23), residues: 444 loop : -2.13 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.009 0.002 HIS A 655 PHE 0.019 0.002 PHE B 565 TYR 0.035 0.002 TYR A1007 ARG 0.008 0.001 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 376 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 383 average time/residue: 0.2499 time to fit residues: 154.4126 Evaluate side-chains 388 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 368 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1675 time to fit residues: 8.7141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 263 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 272 optimal weight: 0.0020 chunk 170 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 ASN B 965 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17839 Z= 0.180 Angle : 0.569 15.253 24509 Z= 0.312 Chirality : 0.046 0.375 2907 Planarity : 0.004 0.070 3337 Dihedral : 5.005 22.549 2886 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.30 % Favored : 92.67 % Rotamer: Outliers : 1.74 % Allowed : 20.37 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2741 helix: 0.73 (0.22), residues: 598 sheet: -0.86 (0.24), residues: 439 loop : -1.88 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 104 HIS 0.029 0.002 HIS C 49 PHE 0.028 0.001 PHE A 855 TYR 0.032 0.001 TYR A1007 ARG 0.007 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 378 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 386 average time/residue: 0.2447 time to fit residues: 150.8796 Evaluate side-chains 380 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 369 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1466 time to fit residues: 5.4297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 52 optimal weight: 0.3980 chunk 173 optimal weight: 1.9990 chunk 185 optimal weight: 0.0030 chunk 134 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17839 Z= 0.214 Angle : 0.572 9.765 24509 Z= 0.315 Chirality : 0.046 0.176 2907 Planarity : 0.005 0.056 3337 Dihedral : 4.949 23.089 2886 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.65 % Favored : 91.28 % Rotamer: Outliers : 1.74 % Allowed : 21.79 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.16), residues: 2741 helix: 0.61 (0.21), residues: 628 sheet: -0.95 (0.24), residues: 444 loop : -1.95 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 353 HIS 0.012 0.002 HIS C1064 PHE 0.029 0.001 PHE C 898 TYR 0.031 0.002 TYR A1007 ARG 0.008 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 368 time to evaluate : 2.085 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: 16 outliers final: 14 residues processed: 373 average time/residue: 0.2615 time to fit residues: 156.5887 Evaluate side-chains 375 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 361 time to evaluate : 2.011 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1648 time to fit residues: 7.0997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 248 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 238 optimal weight: 0.4980 chunk 254 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 229 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 17839 Z= 0.389 Angle : 0.703 15.101 24509 Z= 0.397 Chirality : 0.049 0.246 2907 Planarity : 0.005 0.064 3337 Dihedral : 5.750 25.838 2886 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.58 % Favored : 89.31 % Rotamer: Outliers : 1.31 % Allowed : 22.77 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 2741 helix: 0.00 (0.21), residues: 627 sheet: -1.08 (0.25), residues: 409 loop : -2.29 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 436 HIS 0.015 0.002 HIS C1064 PHE 0.029 0.002 PHE A 855 TYR 0.057 0.002 TYR A1007 ARG 0.007 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 373 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 379 average time/residue: 0.2627 time to fit residues: 159.6216 Evaluate side-chains 373 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 364 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1652 time to fit residues: 5.3546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 0.3980 chunk 268 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 186 optimal weight: 0.2980 chunk 281 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17839 Z= 0.212 Angle : 0.587 8.143 24509 Z= 0.324 Chirality : 0.046 0.164 2907 Planarity : 0.004 0.051 3337 Dihedral : 5.151 22.785 2886 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.17 % Favored : 91.72 % Rotamer: Outliers : 0.44 % Allowed : 24.62 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.16), residues: 2741 helix: 0.53 (0.22), residues: 618 sheet: -1.04 (0.25), residues: 429 loop : -2.09 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 353 HIS 0.012 0.002 HIS C1064 PHE 0.034 0.002 PHE C 643 TYR 0.037 0.002 TYR A1007 ARG 0.008 0.001 ARG C 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5482 Ramachandran restraints generated. 2741 Oldfield, 0 Emsley, 2741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 370 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 371 average time/residue: 0.2543 time to fit residues: 150.9990 Evaluate side-chains 366 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 364 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1470 time to fit residues: 3.0130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 178 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 207 optimal weight: 0.0570 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 0.0970 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122074 restraints weight = 37357.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125541 restraints weight = 22317.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127888 restraints weight = 14798.031| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17839 Z= 0.176 Angle : 0.567 8.319 24509 Z= 0.311 Chirality : 0.045 0.151 2907 Planarity : 0.004 0.048 3337 Dihedral : 4.861 22.399 2886 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.39 % Favored : 91.54 % Rotamer: Outliers : 0.22 % Allowed : 26.14 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2741 helix: 0.85 (0.22), residues: 606 sheet: -1.01 (0.25), residues: 439 loop : -1.95 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 353 HIS 0.011 0.001 HIS C1064 PHE 0.031 0.001 PHE C 898 TYR 0.045 0.002 TYR B 904 ARG 0.009 0.001 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3683.65 seconds wall clock time: 66 minutes 44.58 seconds (4004.58 seconds total)