Starting phenix.real_space_refine on Sat Feb 17 04:58:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/02_2024/8fez_29035_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/02_2024/8fez_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_29035/02_2024/8fez_29035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/02_2024/8fez_29035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/02_2024/8fez_29035_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fez_29035/02_2024/8fez_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.29, per 1000 atoms: 0.59 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: 7.22 Conformation dependent library (CDL) restraints added in 3.9 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: 2.61 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: 6.87 Time building geometry restraints manager: 7.83 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 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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: 1.040 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: 4.540 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 50.900 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.080 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.730 ------------------------------------------------------------------------------- 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 : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.6934 (m-80) cc_final: 0.6714 (m-80) REVERT: A 802 PHE cc_start: 0.8153 (m-80) cc_final: 0.7847 (m-80) REVERT: A 905 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7424 (mtp85) REVERT: A 1028 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8430 (mtpp) REVERT: A 1062 PHE cc_start: 0.8246 (m-80) cc_final: 0.7924 (m-80) REVERT: A 1064 HIS cc_start: 0.7401 (m-70) cc_final: 0.7174 (m-70) REVERT: A 1107 ARG cc_start: 0.7257 (mtm180) cc_final: 0.7039 (mtm-85) REVERT: A 1135 ASN cc_start: 0.7738 (t0) cc_final: 0.7476 (t0) REVERT: B 220 PHE cc_start: 0.7746 (m-80) cc_final: 0.7517 (m-80) REVERT: B 329 PHE cc_start: 0.7246 (m-80) cc_final: 0.6922 (m-80) REVERT: B 585 LEU cc_start: 0.7119 (mt) cc_final: 0.6888 (mm) REVERT: B 733 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8367 (mtmt) REVERT: B 741 TYR cc_start: 0.7565 (t80) cc_final: 0.7219 (t80) REVERT: B 787 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6697 (mm-40) REVERT: B 873 TYR cc_start: 0.8183 (m-80) cc_final: 0.7911 (m-80) REVERT: B 959 LEU cc_start: 0.8897 (mt) cc_final: 0.8503 (mm) REVERT: B 1033 VAL cc_start: 0.8047 (p) cc_final: 0.7791 (m) REVERT: B 1060 VAL cc_start: 0.8330 (p) cc_final: 0.8061 (t) REVERT: B 1141 LEU cc_start: 0.7570 (mt) cc_final: 0.6559 (pt) REVERT: C 64 TRP cc_start: 0.7369 (p-90) cc_final: 0.7095 (p-90) REVERT: C 577 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7658 (mtp85) outliers start: 2 outliers final: 1 residues processed: 371 average time/residue: 0.2414 time to fit residues: 142.4618 Evaluate side-chains 318 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 797 PHE 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: 9.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 144 optimal weight: 0.0170 chunk 114 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B 49 HIS B 422 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN C 641 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17839 Z= 0.232 Angle : 0.649 10.841 24509 Z= 0.366 Chirality : 0.047 0.204 2907 Planarity : 0.005 0.063 3337 Dihedral : 5.678 56.986 2888 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 2.83 % Allowed : 9.59 % Favored : 87.58 % 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: -1.28 (0.15), residues: 2741 helix: 0.41 (0.20), residues: 621 sheet: -0.28 (0.23), residues: 450 loop : -1.57 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 353 HIS 0.009 0.002 HIS A 655 PHE 0.022 0.002 PHE B 927 TYR 0.033 0.002 TYR B 660 ARG 0.003 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 368 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 342 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7053 (tp-100) cc_final: 0.6799 (tp-100) REVERT: A 498 GLN cc_start: 0.8506 (mm110) cc_final: 0.7684 (mp10) REVERT: A 578 ASP cc_start: 0.7143 (t0) cc_final: 0.6879 (t70) REVERT: A 722 VAL cc_start: 0.8992 (t) cc_final: 0.8653 (m) REVERT: A 774 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7342 (mm-40) REVERT: A 802 PHE cc_start: 0.7783 (m-80) cc_final: 0.7410 (m-80) REVERT: A 898 PHE cc_start: 0.7927 (t80) cc_final: 0.7604 (t80) REVERT: A 905 ARG cc_start: 0.7672 (mtt90) cc_final: 0.7393 (mtp85) REVERT: A 906 PHE cc_start: 0.7868 (m-80) cc_final: 0.7458 (m-80) REVERT: A 907 ASN cc_start: 0.8124 (t0) cc_final: 0.7866 (m-40) REVERT: A 916 PHE cc_start: 0.5824 (p90) cc_final: 0.5610 (p90) REVERT: A 1028 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8296 (mttm) REVERT: A 1039 ARG cc_start: 0.7408 (ttm170) cc_final: 0.7207 (ttm-80) REVERT: A 1064 HIS cc_start: 0.7187 (m-70) cc_final: 0.6913 (m-70) REVERT: A 1107 ARG cc_start: 0.7394 (mtm110) cc_final: 0.7085 (mtm-85) REVERT: A 1135 ASN cc_start: 0.7824 (t0) cc_final: 0.7566 (t0) REVERT: B 37 TYR cc_start: 0.6605 (p90) cc_final: 0.5934 (p90) REVERT: B 170 TYR cc_start: 0.7190 (t80) cc_final: 0.6927 (t80) REVERT: B 329 PHE cc_start: 0.7462 (m-80) cc_final: 0.7201 (m-80) REVERT: B 733 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8354 (mtmt) REVERT: B 765 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.7837 (ttp80) REVERT: B 787 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7127 (mm110) REVERT: B 898 PHE cc_start: 0.8294 (t80) cc_final: 0.8002 (t80) REVERT: B 1007 TYR cc_start: 0.8810 (t80) cc_final: 0.8521 (t80) REVERT: B 1060 VAL cc_start: 0.8267 (p) cc_final: 0.7939 (t) REVERT: B 1071 GLN cc_start: 0.8130 (mp10) cc_final: 0.7217 (mp10) REVERT: C 37 TYR cc_start: 0.8102 (p90) cc_final: 0.7628 (p90) REVERT: C 204 TYR cc_start: 0.7394 (m-80) cc_final: 0.7040 (m-80) REVERT: C 275 PHE cc_start: 0.7757 (m-80) cc_final: 0.7398 (m-80) REVERT: C 732 THR cc_start: 0.8391 (m) cc_final: 0.8002 (p) REVERT: C 1100 THR cc_start: 0.3620 (OUTLIER) cc_final: 0.2605 (m) REVERT: C 1110 TYR cc_start: 0.6954 (t80) cc_final: 0.6471 (t80) outliers start: 26 outliers final: 16 residues processed: 356 average time/residue: 0.2481 time to fit residues: 140.2529 Evaluate side-chains 344 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 327 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 953 ASN Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 953 ASN B1088 HIS ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS C1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 17839 Z= 0.374 Angle : 0.717 11.855 24509 Z= 0.411 Chirality : 0.049 0.241 2907 Planarity : 0.005 0.072 3337 Dihedral : 5.944 40.739 2888 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.81 % Favored : 92.16 % Rotamer: Outliers : 4.14 % Allowed : 12.31 % Favored : 83.55 % 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: -1.89 (0.15), residues: 2741 helix: -0.04 (0.20), residues: 610 sheet: -0.83 (0.22), residues: 487 loop : -1.95 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 436 HIS 0.012 0.002 HIS C 49 PHE 0.030 0.002 PHE C1075 TYR 0.027 0.002 TYR A 612 ARG 0.011 0.001 ARG C 577 *********************** 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 405 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 367 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8271 (m-30) cc_final: 0.8035 (m-30) REVERT: A 313 TYR cc_start: 0.8472 (m-80) cc_final: 0.8072 (m-80) REVERT: A 314 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7901 (tp-100) REVERT: A 578 ASP cc_start: 0.6764 (t0) cc_final: 0.6478 (t70) REVERT: A 722 VAL cc_start: 0.8965 (t) cc_final: 0.8639 (m) REVERT: A 802 PHE cc_start: 0.8333 (m-80) cc_final: 0.7984 (m-80) REVERT: A 898 PHE cc_start: 0.7966 (t80) cc_final: 0.7429 (t80) REVERT: A 907 ASN cc_start: 0.8160 (t0) cc_final: 0.7923 (m-40) REVERT: A 1007 TYR cc_start: 0.8327 (t80) cc_final: 0.8071 (t80) REVERT: A 1028 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8394 (mttm) REVERT: A 1107 ARG cc_start: 0.7469 (mtm180) cc_final: 0.7177 (mtm-85) REVERT: A 1135 ASN cc_start: 0.7980 (t0) cc_final: 0.7733 (t0) REVERT: B 170 TYR cc_start: 0.7566 (t80) cc_final: 0.7307 (t80) REVERT: B 269 TYR cc_start: 0.7258 (m-80) cc_final: 0.6933 (m-80) REVERT: B 612 TYR cc_start: 0.8065 (m-80) cc_final: 0.7724 (m-80) REVERT: B 655 HIS cc_start: 0.8393 (t70) cc_final: 0.7978 (t70) REVERT: B 690 GLN cc_start: 0.7916 (tp40) cc_final: 0.7694 (tp40) REVERT: B 733 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8402 (mtmt) REVERT: B 765 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8182 (ttp80) REVERT: B 787 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7093 (mm-40) REVERT: B 800 PHE cc_start: 0.8214 (m-80) cc_final: 0.7791 (m-10) REVERT: B 898 PHE cc_start: 0.8386 (t80) cc_final: 0.7801 (t80) REVERT: B 1048 HIS cc_start: 0.7530 (t70) cc_final: 0.7174 (t-170) REVERT: B 1060 VAL cc_start: 0.8323 (p) cc_final: 0.7976 (t) REVERT: B 1071 GLN cc_start: 0.8604 (mp10) cc_final: 0.7898 (mt0) REVERT: C 204 TYR cc_start: 0.7537 (m-80) cc_final: 0.6958 (m-80) REVERT: C 205 SER cc_start: 0.8307 (t) cc_final: 0.8033 (t) REVERT: C 732 THR cc_start: 0.8702 (m) cc_final: 0.8364 (p) REVERT: C 1007 TYR cc_start: 0.8812 (t80) cc_final: 0.7580 (t80) REVERT: C 1110 TYR cc_start: 0.6905 (t80) cc_final: 0.6426 (t80) outliers start: 38 outliers final: 29 residues processed: 383 average time/residue: 0.2340 time to fit residues: 142.9890 Evaluate side-chains 382 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 353 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 953 ASN Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 254 optimal weight: 0.2980 chunk 193 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 chunk 273 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17839 Z= 0.167 Angle : 0.551 6.899 24509 Z= 0.303 Chirality : 0.045 0.150 2907 Planarity : 0.004 0.056 3337 Dihedral : 5.139 35.889 2888 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 3.27 % Allowed : 15.58 % Favored : 81.15 % 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: -1.56 (0.15), residues: 2741 helix: 0.67 (0.21), residues: 605 sheet: -0.78 (0.22), residues: 475 loop : -1.86 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1102 HIS 0.015 0.001 HIS C 49 PHE 0.026 0.001 PHE B 92 TYR 0.024 0.001 TYR A 741 ARG 0.005 0.000 ARG B1039 *********************** 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 405 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 375 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8275 (m-30) cc_final: 0.8052 (m-30) REVERT: A 314 GLN cc_start: 0.8090 (tp-100) cc_final: 0.7855 (tp40) REVERT: A 498 GLN cc_start: 0.8650 (mm110) cc_final: 0.7719 (mp10) REVERT: A 578 ASP cc_start: 0.7166 (t0) cc_final: 0.6882 (t70) REVERT: A 722 VAL cc_start: 0.8860 (t) cc_final: 0.8567 (m) REVERT: A 802 PHE cc_start: 0.7952 (m-80) cc_final: 0.7658 (m-80) REVERT: A 1028 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8351 (mttm) REVERT: A 1135 ASN cc_start: 0.8107 (t0) cc_final: 0.7839 (t0) REVERT: B 269 TYR cc_start: 0.7125 (m-80) cc_final: 0.6650 (m-10) REVERT: B 612 TYR cc_start: 0.7905 (m-80) cc_final: 0.7578 (m-80) REVERT: B 642 VAL cc_start: 0.9035 (t) cc_final: 0.8803 (m) REVERT: B 655 HIS cc_start: 0.8348 (t70) cc_final: 0.7873 (t70) REVERT: B 733 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8356 (mtmt) REVERT: B 765 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.8077 (ttp80) REVERT: B 787 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7141 (mm-40) REVERT: B 898 PHE cc_start: 0.8258 (t80) cc_final: 0.7942 (t80) REVERT: B 929 SER cc_start: 0.8550 (m) cc_final: 0.8291 (p) REVERT: B 1048 HIS cc_start: 0.7404 (t70) cc_final: 0.7125 (t-170) REVERT: B 1060 VAL cc_start: 0.8245 (p) cc_final: 0.7996 (t) REVERT: B 1071 GLN cc_start: 0.8456 (mp10) cc_final: 0.7671 (mt0) REVERT: C 37 TYR cc_start: 0.8102 (p90) cc_final: 0.7871 (p90) REVERT: C 205 SER cc_start: 0.8240 (t) cc_final: 0.7930 (t) REVERT: C 610 VAL cc_start: 0.8274 (p) cc_final: 0.7925 (m) REVERT: C 732 THR cc_start: 0.8675 (m) cc_final: 0.8277 (p) REVERT: C 787 GLN cc_start: 0.8254 (pm20) cc_final: 0.7910 (pm20) REVERT: C 898 PHE cc_start: 0.8070 (t80) cc_final: 0.7861 (t80) REVERT: C 916 PHE cc_start: 0.8048 (t80) cc_final: 0.7843 (t80) REVERT: C 1062 PHE cc_start: 0.7601 (m-80) cc_final: 0.7372 (m-80) REVERT: C 1100 THR cc_start: 0.5979 (p) cc_final: 0.4234 (m) outliers start: 30 outliers final: 26 residues processed: 389 average time/residue: 0.2491 time to fit residues: 156.3612 Evaluate side-chains 386 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 360 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 953 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 227 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 203 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 0.1980 chunk 245 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17839 Z= 0.231 Angle : 0.576 7.885 24509 Z= 0.319 Chirality : 0.046 0.155 2907 Planarity : 0.004 0.057 3337 Dihedral : 5.081 31.297 2888 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 3.70 % Allowed : 17.10 % Favored : 79.19 % 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 (0.15), residues: 2741 helix: 0.69 (0.21), residues: 612 sheet: -0.72 (0.23), residues: 470 loop : -1.95 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.012 0.001 HIS C 49 PHE 0.026 0.001 PHE A 800 TYR 0.021 0.002 TYR A1007 ARG 0.011 0.001 ARG B1039 *********************** 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 405 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 371 time to evaluate : 1.979 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: A 290 ASP cc_start: 0.8370 (m-30) cc_final: 0.8154 (m-30) REVERT: A 314 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7760 (tp-100) REVERT: A 578 ASP cc_start: 0.6866 (t0) cc_final: 0.6563 (t70) REVERT: A 722 VAL cc_start: 0.8869 (t) cc_final: 0.8566 (m) REVERT: A 802 PHE cc_start: 0.8085 (m-80) cc_final: 0.7789 (m-80) REVERT: A 1007 TYR cc_start: 0.8190 (t80) cc_final: 0.7948 (t80) REVERT: A 1028 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8389 (mttm) REVERT: A 1039 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7032 (mtt90) REVERT: A 1135 ASN cc_start: 0.7964 (t0) cc_final: 0.7673 (t0) REVERT: B 170 TYR cc_start: 0.7470 (t80) cc_final: 0.6962 (t80) REVERT: B 642 VAL cc_start: 0.9057 (t) cc_final: 0.8818 (m) REVERT: B 655 HIS cc_start: 0.8433 (t70) cc_final: 0.7899 (t70) REVERT: B 733 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8391 (mtmt) REVERT: B 765 ARG cc_start: 0.8419 (mtp-110) cc_final: 0.7946 (ttp80) REVERT: B 787 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7177 (mm-40) REVERT: B 898 PHE cc_start: 0.8299 (t80) cc_final: 0.7979 (t80) REVERT: B 929 SER cc_start: 0.8557 (m) cc_final: 0.8297 (p) REVERT: B 1039 ARG cc_start: 0.7418 (mtp180) cc_final: 0.6960 (mtp180) REVERT: B 1048 HIS cc_start: 0.7475 (t70) cc_final: 0.7143 (t-170) REVERT: B 1060 VAL cc_start: 0.8266 (p) cc_final: 0.7923 (t) REVERT: B 1071 GLN cc_start: 0.8532 (mp10) cc_final: 0.7965 (mt0) REVERT: B 1089 PHE cc_start: 0.7586 (m-10) cc_final: 0.7232 (m-80) REVERT: C 37 TYR cc_start: 0.8138 (p90) cc_final: 0.7929 (p90) REVERT: C 205 SER cc_start: 0.8229 (t) cc_final: 0.7922 (t) REVERT: C 610 VAL cc_start: 0.8257 (p) cc_final: 0.7912 (m) REVERT: C 660 TYR cc_start: 0.7558 (m-80) cc_final: 0.7184 (m-80) REVERT: C 732 THR cc_start: 0.8701 (m) cc_final: 0.8288 (p) REVERT: C 787 GLN cc_start: 0.8252 (pm20) cc_final: 0.7905 (pm20) REVERT: C 898 PHE cc_start: 0.8123 (t80) cc_final: 0.7920 (t80) REVERT: C 1110 TYR cc_start: 0.6840 (t80) cc_final: 0.6407 (t80) outliers start: 34 outliers final: 30 residues processed: 386 average time/residue: 0.2431 time to fit residues: 150.4875 Evaluate side-chains 391 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 361 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 953 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 0.0970 chunk 246 optimal weight: 4.9990 chunk 54 optimal weight: 0.0010 chunk 160 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 22 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 779 GLN C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17839 Z= 0.162 Angle : 0.531 8.157 24509 Z= 0.289 Chirality : 0.045 0.150 2907 Planarity : 0.004 0.053 3337 Dihedral : 4.699 22.180 2886 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 3.70 % Allowed : 18.08 % Favored : 78.21 % 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: -1.39 (0.16), residues: 2741 helix: 1.03 (0.22), residues: 609 sheet: -0.72 (0.23), residues: 479 loop : -1.83 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 353 HIS 0.009 0.001 HIS C1064 PHE 0.021 0.001 PHE B 43 TYR 0.018 0.001 TYR C 91 ARG 0.005 0.001 ARG A1039 *********************** 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: 34 poor density : 370 time to evaluate : 1.827 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 REVERT: A 290 ASP cc_start: 0.8357 (m-30) cc_final: 0.8133 (m-30) REVERT: A 314 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7848 (tp-100) REVERT: A 578 ASP cc_start: 0.7049 (t0) cc_final: 0.6727 (t70) REVERT: A 722 VAL cc_start: 0.8819 (t) cc_final: 0.8524 (m) REVERT: A 802 PHE cc_start: 0.7944 (m-80) cc_final: 0.7584 (m-80) REVERT: A 1135 ASN cc_start: 0.7930 (t0) cc_final: 0.7670 (t0) REVERT: B 603 ASN cc_start: 0.8097 (t0) cc_final: 0.7880 (t0) REVERT: B 642 VAL cc_start: 0.9053 (t) cc_final: 0.8828 (m) REVERT: B 690 GLN cc_start: 0.8124 (tp40) cc_final: 0.7663 (tp40) REVERT: B 733 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8384 (mtmt) REVERT: B 765 ARG cc_start: 0.8368 (mtp-110) cc_final: 0.7924 (ttp80) REVERT: B 787 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7132 (mm-40) REVERT: B 929 SER cc_start: 0.8464 (m) cc_final: 0.8236 (p) REVERT: B 1033 VAL cc_start: 0.7885 (p) cc_final: 0.7588 (m) REVERT: B 1048 HIS cc_start: 0.7426 (t70) cc_final: 0.7111 (t-170) REVERT: B 1060 VAL cc_start: 0.8287 (p) cc_final: 0.7972 (t) REVERT: B 1071 GLN cc_start: 0.8480 (mp10) cc_final: 0.7995 (mt0) REVERT: B 1089 PHE cc_start: 0.7541 (m-10) cc_final: 0.7087 (m-80) REVERT: C 205 SER cc_start: 0.8253 (t) cc_final: 0.7985 (t) REVERT: C 610 VAL cc_start: 0.8239 (p) cc_final: 0.7884 (m) REVERT: C 660 TYR cc_start: 0.7529 (m-80) cc_final: 0.7250 (m-80) REVERT: C 732 THR cc_start: 0.8683 (m) cc_final: 0.8230 (p) REVERT: C 787 GLN cc_start: 0.8222 (pm20) cc_final: 0.7918 (pm20) REVERT: C 898 PHE cc_start: 0.8047 (t80) cc_final: 0.7841 (t80) REVERT: C 1110 TYR cc_start: 0.6838 (t80) cc_final: 0.6444 (t80) outliers start: 34 outliers final: 32 residues processed: 387 average time/residue: 0.2384 time to fit residues: 149.2440 Evaluate side-chains 389 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 357 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 953 ASN Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 263 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 272 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17839 Z= 0.220 Angle : 0.557 7.162 24509 Z= 0.307 Chirality : 0.045 0.212 2907 Planarity : 0.004 0.046 3337 Dihedral : 4.822 23.164 2886 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.37 % Favored : 92.56 % Rotamer: Outliers : 4.58 % Allowed : 18.41 % Favored : 77.02 % 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: -1.47 (0.16), residues: 2741 helix: 0.96 (0.22), residues: 608 sheet: -0.79 (0.23), residues: 463 loop : -1.87 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 353 HIS 0.012 0.002 HIS C1064 PHE 0.021 0.001 PHE C1042 TYR 0.028 0.002 TYR A1007 ARG 0.013 0.001 ARG A1107 *********************** 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 419 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 377 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8375 (m-30) cc_final: 0.8152 (m-30) REVERT: A 394 ASN cc_start: 0.6087 (t0) cc_final: 0.5755 (t0) REVERT: A 578 ASP cc_start: 0.7021 (t0) cc_final: 0.6692 (t70) REVERT: A 722 VAL cc_start: 0.8862 (t) cc_final: 0.8562 (m) REVERT: A 802 PHE cc_start: 0.8046 (m-80) cc_final: 0.7729 (m-80) REVERT: A 1007 TYR cc_start: 0.8189 (t80) cc_final: 0.7825 (t80) REVERT: A 1039 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7154 (mtp85) REVERT: A 1135 ASN cc_start: 0.7815 (t0) cc_final: 0.7563 (t0) REVERT: B 642 VAL cc_start: 0.9098 (t) cc_final: 0.8869 (m) REVERT: B 660 TYR cc_start: 0.8120 (m-80) cc_final: 0.7852 (m-80) REVERT: B 670 ILE cc_start: 0.7813 (mm) cc_final: 0.7575 (mm) REVERT: B 690 GLN cc_start: 0.8112 (tp40) cc_final: 0.7724 (tp40) REVERT: B 733 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8337 (mtmt) REVERT: B 765 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.7934 (ttp80) REVERT: B 787 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7177 (mm-40) REVERT: B 873 TYR cc_start: 0.8463 (m-80) cc_final: 0.7913 (m-80) REVERT: B 929 SER cc_start: 0.8485 (m) cc_final: 0.8244 (p) REVERT: B 1033 VAL cc_start: 0.7875 (p) cc_final: 0.7559 (m) REVERT: B 1048 HIS cc_start: 0.7474 (t70) cc_final: 0.7185 (t-170) REVERT: B 1060 VAL cc_start: 0.8308 (p) cc_final: 0.7958 (t) REVERT: B 1071 GLN cc_start: 0.8550 (mp10) cc_final: 0.8076 (mt0) REVERT: B 1089 PHE cc_start: 0.7569 (m-10) cc_final: 0.7124 (m-80) REVERT: C 49 HIS cc_start: 0.7758 (t70) cc_final: 0.7535 (t70) REVERT: C 205 SER cc_start: 0.8201 (t) cc_final: 0.7884 (t) REVERT: C 610 VAL cc_start: 0.8248 (p) cc_final: 0.7893 (m) REVERT: C 660 TYR cc_start: 0.7533 (m-80) cc_final: 0.7078 (m-80) REVERT: C 732 THR cc_start: 0.8726 (m) cc_final: 0.8298 (p) REVERT: C 787 GLN cc_start: 0.8273 (pm20) cc_final: 0.7994 (pm20) REVERT: C 898 PHE cc_start: 0.8086 (t80) cc_final: 0.7877 (t80) REVERT: C 1110 TYR cc_start: 0.6906 (t80) cc_final: 0.6520 (t80) outliers start: 42 outliers final: 37 residues processed: 398 average time/residue: 0.2592 time to fit residues: 168.1715 Evaluate side-chains 408 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 371 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 953 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17839 Z= 0.327 Angle : 0.642 10.034 24509 Z= 0.362 Chirality : 0.047 0.253 2907 Planarity : 0.005 0.060 3337 Dihedral : 5.456 30.386 2886 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.27 % Favored : 90.62 % Rotamer: Outliers : 4.25 % Allowed : 20.04 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.88 (0.16), residues: 2741 helix: 0.44 (0.21), residues: 622 sheet: -0.97 (0.24), residues: 440 loop : -2.10 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.015 0.002 HIS C1064 PHE 0.024 0.002 PHE C1042 TYR 0.034 0.002 TYR A1007 ARG 0.011 0.001 ARG B1039 *********************** 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 417 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 378 time to evaluate : 1.932 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: A 51 THR cc_start: 0.8137 (t) cc_final: 0.7786 (p) REVERT: A 290 ASP cc_start: 0.8422 (m-30) cc_final: 0.8202 (m-30) REVERT: A 578 ASP cc_start: 0.6822 (t0) cc_final: 0.6511 (t70) REVERT: A 722 VAL cc_start: 0.8908 (t) cc_final: 0.8604 (m) REVERT: A 802 PHE cc_start: 0.8111 (m-80) cc_final: 0.7748 (m-80) REVERT: A 953 ASN cc_start: 0.8531 (t0) cc_final: 0.8169 (t0) REVERT: A 1007 TYR cc_start: 0.8217 (t80) cc_final: 0.7853 (t80) REVERT: A 1039 ARG cc_start: 0.8350 (mtp85) cc_final: 0.7218 (mtp85) REVERT: A 1068 VAL cc_start: 0.8823 (t) cc_final: 0.8478 (m) REVERT: A 1135 ASN cc_start: 0.7818 (t0) cc_final: 0.7597 (t0) REVERT: B 269 TYR cc_start: 0.7208 (m-80) cc_final: 0.6676 (m-80) REVERT: B 642 VAL cc_start: 0.9165 (t) cc_final: 0.8859 (p) REVERT: B 660 TYR cc_start: 0.8175 (m-80) cc_final: 0.7882 (m-80) REVERT: B 670 ILE cc_start: 0.7973 (mm) cc_final: 0.7713 (mm) REVERT: B 733 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8339 (mtmt) REVERT: B 765 ARG cc_start: 0.8502 (mtp-110) cc_final: 0.8136 (ttp80) REVERT: B 787 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7238 (mm-40) REVERT: B 873 TYR cc_start: 0.8507 (m-80) cc_final: 0.7986 (m-80) REVERT: B 929 SER cc_start: 0.8544 (m) cc_final: 0.8314 (p) REVERT: B 1033 VAL cc_start: 0.7858 (p) cc_final: 0.7496 (m) REVERT: B 1048 HIS cc_start: 0.7534 (t70) cc_final: 0.7226 (t-170) REVERT: B 1060 VAL cc_start: 0.8242 (p) cc_final: 0.7916 (t) REVERT: B 1071 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: B 1089 PHE cc_start: 0.7516 (m-10) cc_final: 0.7064 (m-80) REVERT: B 1126 CYS cc_start: 0.6135 (p) cc_final: 0.5927 (p) REVERT: C 49 HIS cc_start: 0.7859 (t70) cc_final: 0.7577 (t70) REVERT: C 205 SER cc_start: 0.8094 (t) cc_final: 0.7799 (t) REVERT: C 610 VAL cc_start: 0.8218 (p) cc_final: 0.7862 (m) REVERT: C 732 THR cc_start: 0.8728 (m) cc_final: 0.8328 (p) REVERT: C 1047 TYR cc_start: 0.7491 (m-80) cc_final: 0.7272 (m-80) REVERT: C 1110 TYR cc_start: 0.6918 (t80) cc_final: 0.6546 (t80) outliers start: 39 outliers final: 33 residues processed: 394 average time/residue: 0.2374 time to fit residues: 150.8954 Evaluate side-chains 403 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 369 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 953 ASN Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 248 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 254 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 253 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** C1064 HIS C1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17839 Z= 0.213 Angle : 0.582 13.370 24509 Z= 0.320 Chirality : 0.046 0.320 2907 Planarity : 0.004 0.075 3337 Dihedral : 5.079 24.633 2886 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 3.70 % Allowed : 21.46 % Favored : 74.84 % 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: -1.73 (0.16), residues: 2741 helix: 0.74 (0.21), residues: 619 sheet: -1.08 (0.24), residues: 455 loop : -2.01 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.010 0.001 HIS C1064 PHE 0.021 0.001 PHE A 855 TYR 0.028 0.002 TYR A1007 ARG 0.008 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 406 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 372 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8141 (t) cc_final: 0.7817 (p) REVERT: A 290 ASP cc_start: 0.8252 (m-30) cc_final: 0.8032 (m-30) REVERT: A 394 ASN cc_start: 0.6132 (t0) cc_final: 0.5809 (t0) REVERT: A 578 ASP cc_start: 0.6766 (t0) cc_final: 0.6460 (t70) REVERT: A 722 VAL cc_start: 0.8859 (t) cc_final: 0.8560 (m) REVERT: A 802 PHE cc_start: 0.7898 (m-80) cc_final: 0.7532 (m-80) REVERT: A 953 ASN cc_start: 0.8436 (t0) cc_final: 0.8112 (t0) REVERT: A 1007 TYR cc_start: 0.8176 (t80) cc_final: 0.7773 (t80) REVERT: A 1039 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7307 (mtp85) REVERT: A 1068 VAL cc_start: 0.8813 (t) cc_final: 0.8425 (m) REVERT: B 269 TYR cc_start: 0.7146 (m-80) cc_final: 0.6915 (m-80) REVERT: B 642 VAL cc_start: 0.9137 (t) cc_final: 0.8834 (p) REVERT: B 660 TYR cc_start: 0.8111 (m-80) cc_final: 0.7831 (m-80) REVERT: B 670 ILE cc_start: 0.7817 (mm) cc_final: 0.7558 (mm) REVERT: B 733 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8291 (mtmt) REVERT: B 765 ARG cc_start: 0.8420 (mtp-110) cc_final: 0.8039 (ttp80) REVERT: B 787 GLN cc_start: 0.7598 (mm-40) cc_final: 0.6862 (mm-40) REVERT: B 873 TYR cc_start: 0.8457 (m-80) cc_final: 0.7910 (m-80) REVERT: B 929 SER cc_start: 0.8472 (m) cc_final: 0.8247 (p) REVERT: B 1048 HIS cc_start: 0.7521 (t70) cc_final: 0.7249 (t-170) REVERT: B 1060 VAL cc_start: 0.8237 (p) cc_final: 0.7893 (t) REVERT: B 1071 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: B 1089 PHE cc_start: 0.7512 (m-10) cc_final: 0.7021 (m-80) REVERT: C 49 HIS cc_start: 0.7731 (t70) cc_final: 0.7227 (t-170) REVERT: C 205 SER cc_start: 0.8102 (t) cc_final: 0.7791 (t) REVERT: C 610 VAL cc_start: 0.8181 (p) cc_final: 0.7830 (m) REVERT: C 732 THR cc_start: 0.8747 (m) cc_final: 0.8316 (p) REVERT: C 802 PHE cc_start: 0.7713 (m-80) cc_final: 0.7456 (m-80) REVERT: C 898 PHE cc_start: 0.8214 (t80) cc_final: 0.7974 (t80) REVERT: C 1042 PHE cc_start: 0.8224 (t80) cc_final: 0.7837 (t80) REVERT: C 1110 TYR cc_start: 0.6868 (t80) cc_final: 0.6502 (t80) outliers start: 34 outliers final: 31 residues processed: 386 average time/residue: 0.2345 time to fit residues: 145.5881 Evaluate side-chains 401 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 369 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 953 ASN Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 137 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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** B 370 ASN C 606 ASN ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17839 Z= 0.369 Angle : 0.678 10.922 24509 Z= 0.383 Chirality : 0.049 0.199 2907 Planarity : 0.005 0.059 3337 Dihedral : 5.684 29.807 2886 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.84 % Favored : 89.06 % Rotamer: Outliers : 3.92 % Allowed : 22.00 % Favored : 74.07 % 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: -2.16 (0.15), residues: 2741 helix: 0.25 (0.21), residues: 628 sheet: -1.27 (0.24), residues: 445 loop : -2.27 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 436 HIS 0.015 0.002 HIS C 49 PHE 0.024 0.002 PHE B 43 TYR 0.034 0.002 TYR B 904 ARG 0.009 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 411 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 375 time to evaluate : 1.839 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 REVERT: A 51 THR cc_start: 0.8122 (t) cc_final: 0.7801 (p) REVERT: A 290 ASP cc_start: 0.8235 (m-30) cc_final: 0.8008 (m-30) REVERT: A 578 ASP cc_start: 0.6759 (t0) cc_final: 0.6485 (t70) REVERT: A 722 VAL cc_start: 0.8943 (t) cc_final: 0.8614 (m) REVERT: A 802 PHE cc_start: 0.8265 (m-80) cc_final: 0.7927 (m-80) REVERT: A 953 ASN cc_start: 0.8555 (t0) cc_final: 0.8185 (t0) REVERT: A 1007 TYR cc_start: 0.8239 (t80) cc_final: 0.7851 (t80) REVERT: A 1039 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7386 (mtp85) REVERT: A 1068 VAL cc_start: 0.8813 (t) cc_final: 0.8423 (m) REVERT: B 38 TYR cc_start: 0.7601 (m-80) cc_final: 0.7362 (m-80) REVERT: B 269 TYR cc_start: 0.7190 (m-80) cc_final: 0.6606 (m-10) REVERT: B 642 VAL cc_start: 0.9138 (t) cc_final: 0.8851 (p) REVERT: B 660 TYR cc_start: 0.8154 (m-80) cc_final: 0.7859 (m-80) REVERT: B 670 ILE cc_start: 0.7926 (mm) cc_final: 0.7647 (mm) REVERT: B 733 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8354 (mtmt) REVERT: B 765 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8202 (ttp80) REVERT: B 787 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7206 (mm-40) REVERT: B 873 TYR cc_start: 0.8516 (m-80) cc_final: 0.8030 (m-80) REVERT: B 929 SER cc_start: 0.8552 (m) cc_final: 0.8327 (p) REVERT: B 1007 TYR cc_start: 0.8799 (t80) cc_final: 0.8537 (t80) REVERT: B 1048 HIS cc_start: 0.7574 (t70) cc_final: 0.7286 (t-170) REVERT: B 1060 VAL cc_start: 0.8262 (p) cc_final: 0.7924 (t) REVERT: B 1071 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: B 1089 PHE cc_start: 0.7620 (m-10) cc_final: 0.7139 (m-80) REVERT: B 1091 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.7768 (tpp80) REVERT: C 49 HIS cc_start: 0.7846 (t70) cc_final: 0.7565 (t70) REVERT: C 205 SER cc_start: 0.8042 (t) cc_final: 0.7760 (t) REVERT: C 353 TRP cc_start: 0.5295 (OUTLIER) cc_final: 0.4840 (p-90) REVERT: C 732 THR cc_start: 0.8811 (m) cc_final: 0.8420 (p) REVERT: C 904 TYR cc_start: 0.7425 (m-80) cc_final: 0.7062 (m-80) REVERT: C 1110 TYR cc_start: 0.6902 (t80) cc_final: 0.6534 (t80) outliers start: 36 outliers final: 32 residues processed: 391 average time/residue: 0.2452 time to fit residues: 154.1728 Evaluate side-chains 398 residues out of total 2499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 364 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 953 ASN Chi-restraints excluded: chain C residue 1103 PHE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 178 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.170396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.157929 restraints weight = 47524.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.157202 restraints weight = 45435.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.157325 restraints weight = 37477.525| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17839 Z= 0.314 Angle : 0.640 10.003 24509 Z= 0.358 Chirality : 0.047 0.189 2907 Planarity : 0.005 0.052 3337 Dihedral : 5.559 28.692 2886 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.41 % Favored : 90.48 % Rotamer: Outliers : 4.25 % Allowed : 22.22 % Favored : 73.53 % 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: -2.15 (0.16), residues: 2741 helix: 0.36 (0.21), residues: 622 sheet: -1.31 (0.24), residues: 430 loop : -2.29 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 436 HIS 0.013 0.002 HIS A1064 PHE 0.021 0.002 PHE A 855 TYR 0.030 0.002 TYR A1007 ARG 0.008 0.001 ARG C 577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3648.94 seconds wall clock time: 66 minutes 13.24 seconds (3973.24 seconds total)