Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 20:29:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2023/6vsj_21377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2023/6vsj_21377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2023/6vsj_21377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2023/6vsj_21377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2023/6vsj_21377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2023/6vsj_21377.pdb" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 162 5.16 5 C 18189 2.51 5 N 4860 2.21 5 O 5541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 831": "NH1" <-> "NH2" Residue "A GLU 1077": "OE1" <-> "OE2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 831": "NH1" <-> "NH2" Residue "B GLU 1077": "OE1" <-> "OE2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "C PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C ARG 383": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C GLU 514": "OE1" <-> "OE2" Residue "C ARG 767": "NH1" <-> "NH2" Residue "C ARG 831": "NH1" <-> "NH2" Residue "C GLU 1077": "OE1" <-> "OE2" Residue "C ARG 1137": "NH1" <-> "NH2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 127": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28752 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8678 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1073} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "B" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8678 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1073} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "C" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8678 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1073} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.37, per 1000 atoms: 0.50 Number of scatterers: 28752 At special positions: 0 Unit cell: (171.72, 170.66, 156.88, 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 162 16.00 O 5541 8.00 N 4860 7.00 C 18189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 158 " distance=2.02 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 187 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 246 " distance=2.04 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.05 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 564 " distance=2.06 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 547 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 706 " distance=2.02 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS A 780 " - pdb=" SG CYS A 786 " distance=2.02 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1093 " distance=2.04 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 158 " distance=2.02 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 284 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 425 " distance=2.05 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 564 " distance=2.06 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 706 " distance=2.02 Simple disulfide: pdb=" SG CYS B 775 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 780 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1093 " distance=2.04 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 158 " distance=2.02 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 246 " distance=2.04 Simple disulfide: pdb=" SG CYS C 284 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 425 " distance=2.05 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 564 " distance=2.06 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 507 " distance=2.04 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 547 " distance=2.04 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 706 " distance=2.02 Simple disulfide: pdb=" SG CYS C 775 " - pdb=" SG CYS C 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 780 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1093 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 192 " " NAG A1302 " - " ASN A 435 " " NAG B1301 " - " ASN B 192 " " NAG B1302 " - " ASN B 435 " " NAG C1301 " - " ASN C 192 " " NAG C1302 " - " ASN C 435 " " NAG D 301 " - " ASN D 89 " " NAG E 301 " - " ASN E 89 " " NAG F 301 " - " ASN F 89 " Time building additional restraints: 10.93 Conformation dependent library (CDL) restraints added in 4.0 seconds 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 69 sheets defined 23.7% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.769A pdb=" N LYS A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 357 through 365 removed outlier: 3.504A pdb=" N TYR A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.864A pdb=" N LEU A 403 " --> pdb=" O GLN A 400 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 404 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.247A pdb=" N GLY A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 664 removed outlier: 3.556A pdb=" N PHE A 662 " --> pdb=" O CYS A 658 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 664 " --> pdb=" O TYR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 780 removed outlier: 3.517A pdb=" N PHE A 778 " --> pdb=" O ASP A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 791 removed outlier: 3.892A pdb=" N ARG A 787 " --> pdb=" O ASN A 783 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 788 " --> pdb=" O THR A 784 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 823 removed outlier: 3.744A pdb=" N CYS A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 removed outlier: 3.921A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 896 removed outlier: 3.862A pdb=" N GLU A 889 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 895 " --> pdb=" O TYR A 891 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 910 removed outlier: 3.562A pdb=" N ASN A 910 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 934 Processing helix chain 'A' and resid 947 through 956 removed outlier: 4.292A pdb=" N GLN A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 959 No H-bonds generated for 'chain 'A' and resid 957 through 959' Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.597A pdb=" N LEU A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 989 removed outlier: 4.303A pdb=" N LYS A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1015 removed outlier: 3.611A pdb=" N LYS A 997 " --> pdb=" O SER A 993 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1026 through 1034 removed outlier: 3.684A pdb=" N THR A1032 " --> pdb=" O GLN A1028 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1034 " --> pdb=" O ILE A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1082 removed outlier: 3.593A pdb=" N ALA A1041 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.536A pdb=" N MET D 117 " --> pdb=" O MET D 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.770A pdb=" N LYS B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 357 through 365 removed outlier: 3.504A pdb=" N TYR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.864A pdb=" N LEU B 403 " --> pdb=" O GLN B 400 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 404 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.248A pdb=" N GLY B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 removed outlier: 3.557A pdb=" N PHE B 662 " --> pdb=" O CYS B 658 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 663 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 664 " --> pdb=" O TYR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 780 removed outlier: 3.517A pdb=" N PHE B 778 " --> pdb=" O ASP B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 791 removed outlier: 3.893A pdb=" N ARG B 787 " --> pdb=" O ASN B 783 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 788 " --> pdb=" O THR B 784 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 789 " --> pdb=" O ALA B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 823 removed outlier: 3.743A pdb=" N CYS B 797 " --> pdb=" O TYR B 793 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 817 " --> pdb=" O ASN B 813 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 822 " --> pdb=" O VAL B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 880 removed outlier: 3.920A pdb=" N ASP B 874 " --> pdb=" O SER B 870 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 896 removed outlier: 3.862A pdb=" N GLU B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 893 " --> pdb=" O GLU B 889 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS B 894 " --> pdb=" O ALA B 890 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR B 895 " --> pdb=" O TYR B 891 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY B 896 " --> pdb=" O ASN B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 910 removed outlier: 3.561A pdb=" N ASN B 910 " --> pdb=" O VAL B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 934 Processing helix chain 'B' and resid 947 through 956 removed outlier: 4.292A pdb=" N GLN B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 959 No H-bonds generated for 'chain 'B' and resid 957 through 959' Processing helix chain 'B' and resid 961 through 966 removed outlier: 3.598A pdb=" N LEU B 966 " --> pdb=" O THR B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 989 removed outlier: 4.303A pdb=" N LYS B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1015 removed outlier: 3.609A pdb=" N LYS B 997 " --> pdb=" O SER B 993 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 998 " --> pdb=" O ALA B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1018 No H-bonds generated for 'chain 'B' and resid 1016 through 1018' Processing helix chain 'B' and resid 1026 through 1034 removed outlier: 3.685A pdb=" N THR B1032 " --> pdb=" O GLN B1028 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B1033 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B1034 " --> pdb=" O ILE B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1082 removed outlier: 3.594A pdb=" N ALA B1041 " --> pdb=" O VAL B1037 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP B1044 " --> pdb=" O LYS B1040 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B1045 " --> pdb=" O ALA B1041 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B1046 " --> pdb=" O GLN B1042 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 113 through 117 removed outlier: 3.536A pdb=" N MET E 117 " --> pdb=" O MET E 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.770A pdb=" N LYS C 293 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 357 through 365 removed outlier: 3.504A pdb=" N TYR C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.864A pdb=" N LEU C 403 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 404 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'C' and resid 444 through 451 removed outlier: 4.248A pdb=" N GLY C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 664 removed outlier: 3.556A pdb=" N PHE C 662 " --> pdb=" O CYS C 658 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 663 " --> pdb=" O SER C 659 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN C 664 " --> pdb=" O TYR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 780 removed outlier: 3.517A pdb=" N PHE C 778 " --> pdb=" O ASP C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 791 removed outlier: 3.893A pdb=" N ARG C 787 " --> pdb=" O ASN C 783 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 788 " --> pdb=" O THR C 784 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN C 789 " --> pdb=" O ALA C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 823 removed outlier: 3.743A pdb=" N CYS C 797 " --> pdb=" O TYR C 793 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN C 805 " --> pdb=" O ASN C 801 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 817 " --> pdb=" O ASN C 813 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 822 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 880 removed outlier: 3.921A pdb=" N ASP C 874 " --> pdb=" O SER C 870 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 896 removed outlier: 3.862A pdb=" N GLU C 889 " --> pdb=" O VAL C 885 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 893 " --> pdb=" O GLU C 889 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS C 894 " --> pdb=" O ALA C 890 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR C 895 " --> pdb=" O TYR C 891 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY C 896 " --> pdb=" O ASN C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 910 removed outlier: 3.561A pdb=" N ASN C 910 " --> pdb=" O VAL C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 934 Processing helix chain 'C' and resid 947 through 956 removed outlier: 4.292A pdb=" N GLN C 953 " --> pdb=" O SER C 949 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 959 No H-bonds generated for 'chain 'C' and resid 957 through 959' Processing helix chain 'C' and resid 961 through 966 removed outlier: 3.598A pdb=" N LEU C 966 " --> pdb=" O THR C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 989 removed outlier: 4.303A pdb=" N LYS C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP C 989 " --> pdb=" O GLN C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1015 removed outlier: 3.609A pdb=" N LYS C 997 " --> pdb=" O SER C 993 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE C 998 " --> pdb=" O ALA C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1018 No H-bonds generated for 'chain 'C' and resid 1016 through 1018' Processing helix chain 'C' and resid 1026 through 1034 removed outlier: 3.684A pdb=" N THR C1032 " --> pdb=" O GLN C1028 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C1033 " --> pdb=" O GLU C1029 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C1034 " --> pdb=" O ILE C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1082 removed outlier: 3.594A pdb=" N ALA C1041 " --> pdb=" O VAL C1037 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP C1044 " --> pdb=" O LYS C1040 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C1045 " --> pdb=" O ALA C1041 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C1046 " --> pdb=" O GLN C1042 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 113 through 117 removed outlier: 3.536A pdb=" N MET F 117 " --> pdb=" O MET F 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.732A pdb=" N ASN A 26 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 69 removed outlier: 3.784A pdb=" N ARG A 266 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.522A pdb=" N GLY A 83 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 163 " --> pdb=" O ILE A 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 226 removed outlier: 3.513A pdb=" N THR A 225 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 106 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 261 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG A 257 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 141 removed outlier: 3.635A pdb=" N VAL A 127 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 removed outlier: 7.285A pdb=" N VAL A 152 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 188 " --> pdb=" O VAL A 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.572A pdb=" N THR A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AB2, first strand: chain 'A' and resid 347 through 351 removed outlier: 4.328A pdb=" N GLU A 347 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 392 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 390 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 366 through 369 removed outlier: 3.796A pdb=" N GLN A 366 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS A 428 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 431 " --> pdb=" O CYS A 547 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 547 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 464 through 468 Processing sheet with id=AB5, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AB6, first strand: chain 'A' and resid 517 through 518 removed outlier: 3.765A pdb=" N ILE A 527 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 581 through 585 removed outlier: 3.505A pdb=" N GLY A 590 " --> pdb=" O TYR A 583 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A 631 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 630 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN A 617 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 676 through 677 Processing sheet with id=AB9, first strand: chain 'A' and resid 688 through 694 removed outlier: 7.034A pdb=" N ASN A 688 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 727 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N THR A 690 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 724 " --> pdb=" O ASP A 708 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 708 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 705 " --> pdb=" O MET A 701 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 756 through 758 Processing sheet with id=AC2, first strand: chain 'A' and resid 761 through 763 removed outlier: 3.730A pdb=" N GLU A 762 " --> pdb=" O PHE A1112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 770 through 772 removed outlier: 4.281A pdb=" N LYS A 770 " --> pdb=" O LEU A 915 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 772 " --> pdb=" O LYS A 913 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 913 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 37 through 41 Processing sheet with id=AC5, first strand: chain 'D' and resid 44 through 45 removed outlier: 5.157A pdb=" N THR D 132 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET D 124 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA D 134 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D 118 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE D 65 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG D 81 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP D 67 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.731A pdb=" N ASN B 26 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 64 through 69 removed outlier: 3.783A pdb=" N ARG B 266 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.521A pdb=" N GLY B 83 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B 163 " --> pdb=" O ILE B 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.512A pdb=" N THR B 225 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 106 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 261 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG B 257 " --> pdb=" O GLN B 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 138 through 141 removed outlier: 3.636A pdb=" N VAL B 127 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AD3, first strand: chain 'B' and resid 151 through 153 removed outlier: 7.285A pdb=" N VAL B 152 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 188 " --> pdb=" O VAL B 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.573A pdb=" N THR B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 306 through 307 Processing sheet with id=AD6, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AD7, first strand: chain 'B' and resid 347 through 351 removed outlier: 4.327A pdb=" N GLU B 347 " --> pdb=" O LYS B 392 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 392 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 390 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 366 through 369 removed outlier: 3.797A pdb=" N GLN B 366 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS B 428 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 431 " --> pdb=" O CYS B 547 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 547 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 464 through 468 Processing sheet with id=AE1, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AE2, first strand: chain 'B' and resid 517 through 518 removed outlier: 3.766A pdb=" N ILE B 527 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 581 through 585 removed outlier: 3.506A pdb=" N GLY B 590 " --> pdb=" O TYR B 583 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B 631 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 630 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN B 617 " --> pdb=" O ILE B 630 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 676 through 677 Processing sheet with id=AE5, first strand: chain 'B' and resid 688 through 694 removed outlier: 7.035A pdb=" N ASN B 688 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR B 727 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N THR B 690 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 724 " --> pdb=" O ASP B 708 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 708 " --> pdb=" O ARG B 724 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 705 " --> pdb=" O MET B 701 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 756 through 758 Processing sheet with id=AE7, first strand: chain 'B' and resid 761 through 763 removed outlier: 3.729A pdb=" N GLU B 762 " --> pdb=" O PHE B1112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 770 through 772 removed outlier: 4.281A pdb=" N LYS B 770 " --> pdb=" O LEU B 915 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B 772 " --> pdb=" O LYS B 913 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 913 " --> pdb=" O THR B 772 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 37 through 41 Processing sheet with id=AF1, first strand: chain 'E' and resid 44 through 45 removed outlier: 5.158A pdb=" N THR E 132 " --> pdb=" O MET E 124 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET E 124 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA E 134 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 118 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE E 65 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG E 81 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP E 67 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 26 through 27 removed outlier: 6.732A pdb=" N ASN C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.784A pdb=" N ARG C 266 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.522A pdb=" N GLY C 83 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 163 " --> pdb=" O ILE C 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.512A pdb=" N THR C 225 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 106 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 261 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG C 257 " --> pdb=" O GLN C 109 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 138 through 141 removed outlier: 3.636A pdb=" N VAL C 127 " --> pdb=" O TYR C 240 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AF8, first strand: chain 'C' and resid 151 through 153 removed outlier: 7.285A pdb=" N VAL C 152 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL C 188 " --> pdb=" O VAL C 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.573A pdb=" N THR C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AG2, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AG3, first strand: chain 'C' and resid 347 through 351 removed outlier: 4.329A pdb=" N GLU C 347 " --> pdb=" O LYS C 392 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C 392 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL C 390 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 366 through 369 removed outlier: 3.796A pdb=" N GLN C 366 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS C 428 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 431 " --> pdb=" O CYS C 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS C 547 " --> pdb=" O LEU C 431 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 464 through 468 Processing sheet with id=AG6, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AG7, first strand: chain 'C' and resid 517 through 518 removed outlier: 3.766A pdb=" N ILE C 527 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 581 through 585 removed outlier: 3.505A pdb=" N GLY C 590 " --> pdb=" O TYR C 583 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG C 631 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 630 " --> pdb=" O ASN C 617 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN C 617 " --> pdb=" O ILE C 630 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AH1, first strand: chain 'C' and resid 688 through 694 removed outlier: 7.035A pdb=" N ASN C 688 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR C 727 " --> pdb=" O ASN C 688 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N THR C 690 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG C 724 " --> pdb=" O ASP C 708 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP C 708 " --> pdb=" O ARG C 724 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 705 " --> pdb=" O MET C 701 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 699 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 756 through 758 Processing sheet with id=AH3, first strand: chain 'C' and resid 761 through 763 removed outlier: 3.729A pdb=" N GLU C 762 " --> pdb=" O PHE C1112 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 770 through 772 removed outlier: 4.281A pdb=" N LYS C 770 " --> pdb=" O LEU C 915 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 772 " --> pdb=" O LYS C 913 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS C 913 " --> pdb=" O THR C 772 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 37 through 41 Processing sheet with id=AH6, first strand: chain 'F' and resid 44 through 45 removed outlier: 5.156A pdb=" N THR F 132 " --> pdb=" O MET F 124 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET F 124 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 134 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY F 118 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE F 65 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG F 81 " --> pdb=" O PHE F 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP F 67 " --> pdb=" O ILE F 79 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2079 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: 13.50 Time building geometry restraints manager: 11.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9404 1.34 - 1.47: 7465 1.47 - 1.59: 12318 1.59 - 1.72: 0 1.72 - 1.84: 207 Bond restraints: 29394 Sorted by residual: bond pdb=" C ASN C 442 " pdb=" N PRO C 443 " ideal model delta sigma weight residual 1.332 1.307 0.025 8.20e-03 1.49e+04 9.44e+00 bond pdb=" C ASN A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.332 1.307 0.025 8.20e-03 1.49e+04 9.16e+00 bond pdb=" C ASN B 442 " pdb=" N PRO B 443 " ideal model delta sigma weight residual 1.332 1.308 0.025 8.20e-03 1.49e+04 9.06e+00 bond pdb=" CB TRP C 346 " pdb=" CG TRP C 346 " ideal model delta sigma weight residual 1.498 1.436 0.062 3.10e-02 1.04e+03 4.02e+00 bond pdb=" CB TRP A 346 " pdb=" CG TRP A 346 " ideal model delta sigma weight residual 1.498 1.437 0.061 3.10e-02 1.04e+03 3.93e+00 ... (remaining 29389 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.70: 821 106.70 - 113.73: 16281 113.73 - 120.76: 12880 120.76 - 127.79: 9834 127.79 - 134.83: 216 Bond angle restraints: 40032 Sorted by residual: angle pdb=" CA CYS B 425 " pdb=" CB CYS B 425 " pdb=" SG CYS B 425 " ideal model delta sigma weight residual 114.40 129.51 -15.11 2.30e+00 1.89e-01 4.32e+01 angle pdb=" CA CYS A 425 " pdb=" CB CYS A 425 " pdb=" SG CYS A 425 " ideal model delta sigma weight residual 114.40 129.46 -15.06 2.30e+00 1.89e-01 4.29e+01 angle pdb=" CA CYS C 425 " pdb=" CB CYS C 425 " pdb=" SG CYS C 425 " ideal model delta sigma weight residual 114.40 129.45 -15.05 2.30e+00 1.89e-01 4.28e+01 angle pdb=" N GLY A 103 " pdb=" CA GLY A 103 " pdb=" C GLY A 103 " ideal model delta sigma weight residual 111.85 117.68 -5.83 1.06e+00 8.90e-01 3.02e+01 angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.85 117.67 -5.82 1.06e+00 8.90e-01 3.01e+01 ... (remaining 40027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 15043 16.60 - 33.20: 1834 33.20 - 49.80: 415 49.80 - 66.40: 72 66.40 - 83.01: 27 Dihedral angle restraints: 17391 sinusoidal: 6657 harmonic: 10734 Sorted by residual: dihedral pdb=" CB CYS B 471 " pdb=" SG CYS B 471 " pdb=" SG CYS B 507 " pdb=" CB CYS B 507 " ideal model delta sinusoidal sigma weight residual -86.00 -164.59 78.59 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS A 471 " pdb=" SG CYS A 471 " pdb=" SG CYS A 507 " pdb=" CB CYS A 507 " ideal model delta sinusoidal sigma weight residual -86.00 -164.58 78.58 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS C 471 " pdb=" SG CYS C 471 " pdb=" SG CYS C 507 " pdb=" CB CYS C 507 " ideal model delta sinusoidal sigma weight residual -86.00 -164.53 78.53 1 1.00e+01 1.00e-02 7.69e+01 ... (remaining 17388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3621 0.069 - 0.137: 800 0.137 - 0.206: 97 0.206 - 0.274: 12 0.274 - 0.343: 6 Chirality restraints: 4536 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 435 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 435 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 435 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 4533 not shown) Planarity restraints: 5217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 938 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO A 939 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 939 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 939 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 938 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO B 939 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 939 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 939 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 938 " 0.059 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO C 939 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 939 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 939 " 0.050 5.00e-02 4.00e+02 ... (remaining 5214 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5061 2.75 - 3.29: 27184 3.29 - 3.82: 47044 3.82 - 4.36: 53491 4.36 - 4.90: 89461 Nonbonded interactions: 222241 Sorted by model distance: nonbonded pdb=" OH TYR C1117 " pdb=" OG SER C1159 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR A1117 " pdb=" OG SER A1159 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR B1117 " pdb=" OG SER B1159 " model vdw 2.212 2.440 nonbonded pdb=" O SER B1158 " pdb=" OG SER B1158 " model vdw 2.240 2.440 nonbonded pdb=" O SER A1158 " pdb=" OG SER A1158 " model vdw 2.241 2.440 ... (remaining 222236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.740 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 72.240 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.008 0.066 29394 Z= 0.554 Angle : 1.017 15.109 40032 Z= 0.590 Chirality : 0.058 0.343 4536 Planarity : 0.007 0.089 5208 Dihedral : 15.040 83.006 10383 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.64 % Favored : 90.28 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.11), residues: 3663 helix: -3.80 (0.10), residues: 699 sheet: -2.24 (0.19), residues: 588 loop : -2.65 (0.11), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 437 time to evaluate : 3.254 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 461 average time/residue: 0.4180 time to fit residues: 304.5560 Evaluate side-chains 278 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 262 time to evaluate : 3.154 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2468 time to fit residues: 12.3037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 174 optimal weight: 0.0470 chunk 213 optimal weight: 0.8980 chunk 332 optimal weight: 1.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 172 ASN A 325 ASN A 353 ASN A 374 ASN A 400 GLN A 412 GLN A 447 ASN A 469 GLN A 530 ASN A 544 ASN A 548 GLN A 606 GLN A 643 HIS A 674 ASN A 688 ASN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1018 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 GLN A1104 GLN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN D 128 ASN D 141 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 172 ASN B 353 ASN B 400 GLN B 412 GLN B 447 ASN B 469 GLN B 530 ASN B 544 ASN B 548 GLN B 606 GLN B 674 ASN B 688 ASN B 750 GLN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 GLN B1018 ASN ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN E 141 HIS ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 172 ASN C 353 ASN C 400 GLN C 412 GLN C 447 ASN C 469 GLN C 523 HIS C 530 ASN C 544 ASN C 548 GLN C 606 GLN C 674 ASN C 688 ASN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 ASN C1018 ASN C1086 GLN ** C1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 141 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 29394 Z= 0.230 Angle : 0.660 12.350 40032 Z= 0.357 Chirality : 0.045 0.262 4536 Planarity : 0.005 0.095 5208 Dihedral : 6.433 29.973 4011 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -3.22 (0.12), residues: 3663 helix: -1.76 (0.17), residues: 726 sheet: -2.17 (0.19), residues: 660 loop : -2.34 (0.12), residues: 2277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 332 time to evaluate : 3.025 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 62 residues processed: 405 average time/residue: 0.3733 time to fit residues: 246.8818 Evaluate side-chains 331 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 269 time to evaluate : 3.116 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.2756 time to fit residues: 36.3311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 276 optimal weight: 0.9980 chunk 226 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 332 optimal weight: 0.9990 chunk 359 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 330 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 267 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 643 HIS A 674 ASN A 759 HIS A 953 GLN D 110 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 374 ASN ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 HIS B 953 GLN ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN C 759 HIS C 953 GLN ** C1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 29394 Z= 0.169 Angle : 0.606 11.017 40032 Z= 0.326 Chirality : 0.044 0.205 4536 Planarity : 0.004 0.061 5208 Dihedral : 5.832 28.569 4011 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.73 (0.13), residues: 3663 helix: -0.92 (0.18), residues: 717 sheet: -1.97 (0.19), residues: 609 loop : -2.16 (0.12), residues: 2337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 325 time to evaluate : 3.598 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 26 residues processed: 391 average time/residue: 0.3909 time to fit residues: 255.9788 Evaluate side-chains 289 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 263 time to evaluate : 3.164 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2488 time to fit residues: 16.7172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 334 optimal weight: 0.0980 chunk 353 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 316 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 29394 Z= 0.165 Angle : 0.608 10.252 40032 Z= 0.321 Chirality : 0.044 0.204 4536 Planarity : 0.004 0.059 5208 Dihedral : 5.577 28.521 4011 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.48 (0.13), residues: 3663 helix: -0.59 (0.19), residues: 744 sheet: -1.94 (0.19), residues: 648 loop : -1.99 (0.12), residues: 2271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 311 time to evaluate : 3.259 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 40 residues processed: 348 average time/residue: 0.3764 time to fit residues: 219.3906 Evaluate side-chains 299 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 259 time to evaluate : 3.283 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3003 time to fit residues: 25.7979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 5 optimal weight: 0.0980 chunk 263 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 301 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 317 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 ASN ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN C1114 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 29394 Z= 0.245 Angle : 0.620 10.173 40032 Z= 0.328 Chirality : 0.044 0.186 4536 Planarity : 0.004 0.053 5208 Dihedral : 5.458 28.718 4011 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.34 (0.13), residues: 3663 helix: -0.27 (0.19), residues: 750 sheet: -1.92 (0.19), residues: 636 loop : -1.97 (0.12), residues: 2277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 281 time to evaluate : 3.328 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 41 residues processed: 330 average time/residue: 0.3934 time to fit residues: 215.8623 Evaluate side-chains 297 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 256 time to evaluate : 3.596 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2886 time to fit residues: 26.4970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 9.9990 chunk 318 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 chunk 293 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 0.0170 chunk 117 optimal weight: 10.0000 chunk 185 optimal weight: 0.4980 overall best weight: 2.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 29394 Z= 0.235 Angle : 0.615 9.823 40032 Z= 0.324 Chirality : 0.044 0.198 4536 Planarity : 0.004 0.054 5208 Dihedral : 5.415 28.331 4011 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.22 (0.13), residues: 3663 helix: 0.05 (0.20), residues: 726 sheet: -1.93 (0.19), residues: 636 loop : -1.93 (0.12), residues: 2301 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 275 time to evaluate : 3.273 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 39 residues processed: 323 average time/residue: 0.3805 time to fit residues: 204.9908 Evaluate side-chains 291 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 252 time to evaluate : 3.327 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2799 time to fit residues: 25.0297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 201 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 352 optimal weight: 0.0980 chunk 220 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 HIS E 110 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 29394 Z= 0.166 Angle : 0.595 10.448 40032 Z= 0.313 Chirality : 0.044 0.195 4536 Planarity : 0.004 0.053 5208 Dihedral : 5.224 27.092 4011 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.98 (0.13), residues: 3663 helix: 0.32 (0.20), residues: 726 sheet: -1.66 (0.19), residues: 630 loop : -1.84 (0.13), residues: 2307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 309 time to evaluate : 3.577 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: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 334 average time/residue: 0.3750 time to fit residues: 210.5905 Evaluate side-chains 272 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 260 time to evaluate : 3.410 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2607 time to fit residues: 10.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 277 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 29394 Z= 0.226 Angle : 0.626 12.391 40032 Z= 0.326 Chirality : 0.044 0.179 4536 Planarity : 0.004 0.051 5208 Dihedral : 5.239 27.472 4011 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.99 (0.13), residues: 3663 helix: 0.40 (0.20), residues: 711 sheet: -1.74 (0.19), residues: 636 loop : -1.84 (0.13), residues: 2316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 265 time to evaluate : 3.357 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: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 294 average time/residue: 0.3728 time to fit residues: 185.1290 Evaluate side-chains 279 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 3.522 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2962 time to fit residues: 21.0220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 1.9990 chunk 337 optimal weight: 3.9990 chunk 308 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 258 optimal weight: 0.0970 chunk 100 optimal weight: 8.9990 chunk 297 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 29394 Z= 0.231 Angle : 0.627 11.960 40032 Z= 0.329 Chirality : 0.044 0.180 4536 Planarity : 0.004 0.051 5208 Dihedral : 5.267 27.732 4011 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.97 (0.14), residues: 3663 helix: 0.50 (0.20), residues: 711 sheet: -1.64 (0.19), residues: 651 loop : -1.88 (0.13), residues: 2301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 267 time to evaluate : 3.612 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: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 278 average time/residue: 0.3935 time to fit residues: 185.3980 Evaluate side-chains 256 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 246 time to evaluate : 3.501 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2680 time to fit residues: 9.8728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 2.9990 chunk 347 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 241 optimal weight: 6.9990 chunk 364 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 chunk 290 optimal weight: 7.9990 chunk 30 optimal weight: 0.0370 chunk 224 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 overall best weight: 3.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 352 GLN ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 29394 Z= 0.322 Angle : 0.687 10.809 40032 Z= 0.360 Chirality : 0.046 0.259 4536 Planarity : 0.004 0.053 5208 Dihedral : 5.528 28.501 4011 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.17 (0.13), residues: 3663 helix: 0.42 (0.20), residues: 717 sheet: -1.81 (0.19), residues: 642 loop : -2.04 (0.12), residues: 2304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 3.341 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: symmetry clash outliers start: 21 outliers final: 14 residues processed: 261 average time/residue: 0.3813 time to fit residues: 167.4009 Evaluate side-chains 255 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 241 time to evaluate : 3.304 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2814 time to fit residues: 11.6933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 7.9990 chunk 309 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.086465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070006 restraints weight = 89045.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072258 restraints weight = 52398.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073837 restraints weight = 36369.340| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 29394 Z= 0.350 Angle : 0.699 10.419 40032 Z= 0.369 Chirality : 0.046 0.227 4536 Planarity : 0.004 0.053 5208 Dihedral : 5.643 28.288 4011 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.26 (0.13), residues: 3663 helix: 0.45 (0.20), residues: 708 sheet: -1.92 (0.19), residues: 633 loop : -2.12 (0.12), residues: 2322 =============================================================================== Job complete usr+sys time: 4958.55 seconds wall clock time: 92 minutes 16.01 seconds (5536.01 seconds total)