Starting phenix.real_space_refine on Sat Apr 13 13:16:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2024/6vsj_21377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2024/6vsj_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_2024/6vsj_21377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2024/6vsj_21377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2024/6vsj_21377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vsj_21377/04_2024/6vsj_21377.pdb" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 9 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.38, 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: 11.03 Conformation dependent library (CDL) restraints added in 4.8 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: 3.42 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: 11.81 Time building geometry restraints manager: 12.00 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: 15259 16.60 - 33.20: 1846 33.20 - 49.80: 427 49.80 - 66.40: 84 66.40 - 83.01: 27 Dihedral angle restraints: 17643 sinusoidal: 6909 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 17640 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: 2.230 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: 0.030 Extract box with map and model: 8.650 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 72.940 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.360 ------------------------------------------------------------------------------- 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 : 15.071 83.006 10635 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 % Allowed : 11.40 % Favored : 87.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 334 HIS 0.007 0.002 HIS A 205 PHE 0.029 0.003 PHE C 393 TYR 0.028 0.003 TYR A 203 ARG 0.013 0.001 ARG A 668 *********************** 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 : 3.169 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 REVERT: A 26 ASN cc_start: 0.8311 (t0) cc_final: 0.7788 (t0) REVERT: A 137 TYR cc_start: 0.8770 (m-80) cc_final: 0.8272 (m-10) REVERT: A 149 MET cc_start: 0.8374 (ttm) cc_final: 0.8060 (mtp) REVERT: A 399 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8317 (mmp80) REVERT: A 431 LEU cc_start: 0.8806 (mt) cc_final: 0.8511 (mt) REVERT: A 748 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 749 MET cc_start: 0.7229 (mtt) cc_final: 0.6595 (mtt) REVERT: A 1029 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8293 (tm-30) REVERT: A 1068 ILE cc_start: 0.9655 (mt) cc_final: 0.9449 (mm) REVERT: A 1086 GLN cc_start: 0.8334 (pt0) cc_final: 0.8098 (pp30) REVERT: A 1091 ASN cc_start: 0.7834 (t0) cc_final: 0.6911 (t0) REVERT: D 110 GLN cc_start: 0.7215 (mt0) cc_final: 0.6946 (mm-40) REVERT: D 120 TYR cc_start: 0.6796 (m-80) cc_final: 0.6423 (m-80) REVERT: D 124 MET cc_start: 0.7122 (tmm) cc_final: 0.6444 (tmm) REVERT: B 26 ASN cc_start: 0.8474 (t0) cc_final: 0.7947 (t0) REVERT: B 149 MET cc_start: 0.8398 (ttm) cc_final: 0.8059 (mtp) REVERT: B 184 PRO cc_start: 0.8500 (Cg_exo) cc_final: 0.8233 (Cg_endo) REVERT: B 370 LEU cc_start: 0.9652 (tp) cc_final: 0.9368 (tt) REVERT: B 431 LEU cc_start: 0.8706 (mt) cc_final: 0.8384 (mt) REVERT: B 1029 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 1086 GLN cc_start: 0.8300 (pt0) cc_final: 0.8053 (pp30) REVERT: B 1091 ASN cc_start: 0.7707 (t0) cc_final: 0.6780 (t0) REVERT: E 120 TYR cc_start: 0.6890 (m-80) cc_final: 0.5392 (m-80) REVERT: E 124 MET cc_start: 0.6943 (tmm) cc_final: 0.6506 (tmm) REVERT: C 26 ASN cc_start: 0.8693 (t0) cc_final: 0.8114 (t0) REVERT: C 149 MET cc_start: 0.8323 (ttm) cc_final: 0.8108 (mtp) REVERT: C 184 PRO cc_start: 0.8564 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: C 291 GLU cc_start: 0.8834 (tp30) cc_final: 0.8395 (tp30) REVERT: C 431 LEU cc_start: 0.8916 (mt) cc_final: 0.8685 (mt) REVERT: C 747 TYR cc_start: 0.6150 (m-10) cc_final: 0.5582 (m-80) REVERT: C 940 TRP cc_start: 0.6570 (t-100) cc_final: 0.6274 (t-100) REVERT: C 954 TYR cc_start: 0.8232 (m-10) cc_final: 0.8004 (m-80) REVERT: C 1015 GLN cc_start: 0.8992 (tp40) cc_final: 0.8753 (mm-40) REVERT: C 1064 ASP cc_start: 0.8477 (t0) cc_final: 0.8247 (t0) REVERT: C 1086 GLN cc_start: 0.8514 (pt0) cc_final: 0.8201 (pp30) REVERT: C 1091 ASN cc_start: 0.8037 (t0) cc_final: 0.7216 (t0) REVERT: F 120 TYR cc_start: 0.6711 (m-80) cc_final: 0.5188 (m-80) REVERT: F 124 MET cc_start: 0.7184 (tmm) cc_final: 0.6670 (tmm) outliers start: 30 outliers final: 16 residues processed: 461 average time/residue: 0.4188 time to fit residues: 304.5595 Evaluate side-chains 297 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 281 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 407 ASN Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 1063 SER Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 286 optimal weight: 0.0770 chunk 111 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 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** ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 325 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 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 GLN B1018 ASN ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** 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 C1015 GLN C1018 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN ** C1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 141 HIS Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29394 Z= 0.287 Angle : 0.672 12.596 40032 Z= 0.364 Chirality : 0.045 0.244 4536 Planarity : 0.005 0.091 5208 Dihedral : 7.765 59.084 4286 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.46 % Allowed : 16.95 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.27 (0.12), residues: 3663 helix: -1.74 (0.16), residues: 732 sheet: -2.30 (0.19), residues: 639 loop : -2.37 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 334 HIS 0.004 0.001 HIS C1114 PHE 0.019 0.002 PHE A 393 TYR 0.019 0.002 TYR D 120 ARG 0.006 0.001 ARG E 130 *********************** 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 441 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 332 time to evaluate : 3.183 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: A 26 ASN cc_start: 0.8350 (t0) cc_final: 0.8018 (t0) REVERT: A 184 PRO cc_start: 0.8603 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: A 431 LEU cc_start: 0.8950 (mt) cc_final: 0.8703 (mt) REVERT: A 749 MET cc_start: 0.7261 (mtt) cc_final: 0.6967 (mtt) REVERT: A 1029 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 1064 ASP cc_start: 0.8603 (t0) cc_final: 0.8372 (t0) REVERT: A 1068 ILE cc_start: 0.9451 (mt) cc_final: 0.9202 (mm) REVERT: A 1091 ASN cc_start: 0.7560 (t0) cc_final: 0.6664 (t0) REVERT: D 68 TYR cc_start: 0.8419 (m-80) cc_final: 0.8015 (m-80) REVERT: D 110 GLN cc_start: 0.7306 (mt0) cc_final: 0.7022 (mm-40) REVERT: D 111 MET cc_start: 0.7771 (tmm) cc_final: 0.7550 (tmm) REVERT: D 124 MET cc_start: 0.7153 (tmm) cc_final: 0.6782 (tmm) REVERT: B 26 ASN cc_start: 0.8479 (t0) cc_final: 0.7985 (t0) REVERT: B 184 PRO cc_start: 0.8559 (Cg_exo) cc_final: 0.8306 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8834 (mt) cc_final: 0.8528 (mt) REVERT: B 505 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7942 (p0) REVERT: B 749 MET cc_start: 0.7356 (mtt) cc_final: 0.7153 (mtt) REVERT: B 940 TRP cc_start: 0.6894 (t-100) cc_final: 0.6636 (t-100) REVERT: B 1015 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8161 (mm-40) REVERT: B 1029 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8166 (tm-30) REVERT: B 1091 ASN cc_start: 0.7502 (t0) cc_final: 0.6591 (t0) REVERT: E 111 MET cc_start: 0.7788 (tmm) cc_final: 0.7519 (tmm) REVERT: E 121 THR cc_start: 0.7508 (m) cc_final: 0.7282 (t) REVERT: E 124 MET cc_start: 0.7002 (tmm) cc_final: 0.6745 (tmm) REVERT: C 26 ASN cc_start: 0.8615 (t0) cc_final: 0.8123 (t0) REVERT: C 184 PRO cc_start: 0.8513 (Cg_exo) cc_final: 0.8233 (Cg_endo) REVERT: C 349 LYS cc_start: 0.8255 (tttt) cc_final: 0.8014 (tptm) REVERT: C 431 LEU cc_start: 0.8957 (mt) cc_final: 0.8734 (mt) REVERT: C 637 ARG cc_start: 0.7289 (ptt180) cc_final: 0.4753 (ptt180) REVERT: C 814 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8644 (tpp) REVERT: C 940 TRP cc_start: 0.6857 (t-100) cc_final: 0.6606 (t-100) REVERT: C 1064 ASP cc_start: 0.8558 (t0) cc_final: 0.8298 (t0) REVERT: C 1068 ILE cc_start: 0.9378 (mm) cc_final: 0.9171 (mm) REVERT: C 1091 ASN cc_start: 0.7825 (t0) cc_final: 0.6975 (t0) REVERT: F 88 MET cc_start: 0.8556 (mtm) cc_final: 0.8343 (ptp) REVERT: F 111 MET cc_start: 0.7688 (tmm) cc_final: 0.7428 (tmm) REVERT: F 124 MET cc_start: 0.7327 (tmm) cc_final: 0.7030 (tmm) outliers start: 109 outliers final: 72 residues processed: 408 average time/residue: 0.3919 time to fit residues: 260.7532 Evaluate side-chains 342 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 268 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 407 ASN Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1018 ASN Chi-restraints excluded: chain C residue 1063 SER Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 73 THR 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: 0.9990 chunk 226 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 332 optimal weight: 0.9990 chunk 359 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 374 ASN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 HIS A 953 GLN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 GLN ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN B1048 ASN ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 HIS ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 GLN ** C1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1114 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29394 Z= 0.182 Angle : 0.597 9.959 40032 Z= 0.323 Chirality : 0.044 0.215 4536 Planarity : 0.004 0.084 5208 Dihedral : 6.976 58.247 4280 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.87 % Allowed : 17.56 % Favored : 78.57 % 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: -2.89 (0.13), residues: 3663 helix: -0.93 (0.18), residues: 729 sheet: -2.15 (0.19), residues: 633 loop : -2.28 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.003 0.001 HIS F 56 PHE 0.022 0.001 PHE F 138 TYR 0.016 0.001 TYR C1160 ARG 0.007 0.000 ARG A 637 *********************** 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 438 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 316 time to evaluate : 3.164 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: A 26 ASN cc_start: 0.8538 (t0) cc_final: 0.8078 (t0) REVERT: A 137 TYR cc_start: 0.8646 (m-80) cc_final: 0.8322 (m-10) REVERT: A 184 PRO cc_start: 0.8555 (Cg_exo) cc_final: 0.8342 (Cg_endo) REVERT: A 347 GLU cc_start: 0.8394 (mp0) cc_final: 0.8069 (pm20) REVERT: A 399 ARG cc_start: 0.8692 (mmp80) cc_final: 0.8381 (mmp80) REVERT: A 643 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.7946 (m-70) REVERT: A 748 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6934 (tm-30) REVERT: A 749 MET cc_start: 0.7159 (mtt) cc_final: 0.6473 (mtt) REVERT: A 964 ASN cc_start: 0.8251 (t0) cc_final: 0.8024 (t0) REVERT: A 998 ILE cc_start: 0.9369 (mt) cc_final: 0.9115 (tt) REVERT: A 1029 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8264 (tp30) REVERT: A 1064 ASP cc_start: 0.8645 (t0) cc_final: 0.8381 (t0) REVERT: A 1068 ILE cc_start: 0.9441 (mt) cc_final: 0.9185 (mm) REVERT: A 1086 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7548 (pp30) REVERT: A 1091 ASN cc_start: 0.7619 (t0) cc_final: 0.6684 (t0) REVERT: D 75 ILE cc_start: 0.8133 (mt) cc_final: 0.7646 (mm) REVERT: D 78 GLU cc_start: 0.8301 (pt0) cc_final: 0.7721 (pt0) REVERT: D 110 GLN cc_start: 0.7369 (mt0) cc_final: 0.6987 (mm-40) REVERT: D 111 MET cc_start: 0.7837 (tmm) cc_final: 0.7552 (tmm) REVERT: D 124 MET cc_start: 0.7070 (tmm) cc_final: 0.6723 (tmm) REVERT: B 26 ASN cc_start: 0.8535 (t0) cc_final: 0.7893 (t0) REVERT: B 184 PRO cc_start: 0.8673 (Cg_exo) cc_final: 0.8409 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8814 (mt) cc_final: 0.8576 (mt) REVERT: B 643 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8199 (m-70) REVERT: B 823 MET cc_start: 0.7525 (ttp) cc_final: 0.7311 (ttp) REVERT: B 1015 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8414 (mm-40) REVERT: B 1029 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 1091 ASN cc_start: 0.7461 (t0) cc_final: 0.6447 (t0) REVERT: E 91 THR cc_start: 0.8475 (p) cc_final: 0.8205 (p) REVERT: E 111 MET cc_start: 0.7776 (tmm) cc_final: 0.7447 (tmm) REVERT: E 121 THR cc_start: 0.7341 (m) cc_final: 0.7120 (t) REVERT: E 124 MET cc_start: 0.6857 (tmm) cc_final: 0.6415 (tmm) REVERT: C 26 ASN cc_start: 0.8564 (t0) cc_final: 0.8083 (t0) REVERT: C 184 PRO cc_start: 0.8650 (Cg_exo) cc_final: 0.8350 (Cg_endo) REVERT: C 349 LYS cc_start: 0.8091 (tttt) cc_final: 0.7883 (tptm) REVERT: C 748 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6714 (tm-30) REVERT: C 814 MET cc_start: 0.8875 (mmp) cc_final: 0.8583 (tpp) REVERT: C 940 TRP cc_start: 0.6647 (t-100) cc_final: 0.6199 (t-100) REVERT: C 1064 ASP cc_start: 0.8602 (t0) cc_final: 0.8306 (t0) REVERT: C 1068 ILE cc_start: 0.9398 (mm) cc_final: 0.9132 (mm) REVERT: C 1091 ASN cc_start: 0.7815 (t0) cc_final: 0.6882 (t0) REVERT: C 1111 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8505 (p90) REVERT: F 78 GLU cc_start: 0.8204 (tt0) cc_final: 0.7710 (tm-30) REVERT: F 88 MET cc_start: 0.8597 (mtm) cc_final: 0.8359 (ptp) REVERT: F 111 MET cc_start: 0.7676 (tmm) cc_final: 0.7412 (tmm) REVERT: F 124 MET cc_start: 0.7241 (tmm) cc_final: 0.6954 (tmm) outliers start: 122 outliers final: 61 residues processed: 412 average time/residue: 0.3718 time to fit residues: 254.4098 Evaluate side-chains 346 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 281 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1086 GLN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 1086 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 158 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 334 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 316 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 469 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 ASN ** 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** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** 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** C 953 GLN ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 GLN ** C1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29394 Z= 0.295 Angle : 0.641 10.742 40032 Z= 0.342 Chirality : 0.045 0.210 4536 Planarity : 0.004 0.054 5208 Dihedral : 6.856 58.556 4273 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 4.44 % Allowed : 19.49 % Favored : 76.06 % 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: -2.71 (0.13), residues: 3663 helix: -0.59 (0.19), residues: 747 sheet: -2.16 (0.19), residues: 630 loop : -2.20 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 940 HIS 0.005 0.001 HIS C 759 PHE 0.019 0.002 PHE A 393 TYR 0.018 0.002 TYR B1111 ARG 0.003 0.000 ARG E 130 *********************** 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 431 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 291 time to evaluate : 3.176 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: A 26 ASN cc_start: 0.8486 (t0) cc_final: 0.8082 (t0) REVERT: A 184 PRO cc_start: 0.8549 (Cg_exo) cc_final: 0.8326 (Cg_endo) REVERT: A 347 GLU cc_start: 0.8463 (mp0) cc_final: 0.8205 (pm20) REVERT: A 358 LEU cc_start: 0.8448 (mm) cc_final: 0.8207 (tt) REVERT: A 642 PHE cc_start: 0.8475 (m-80) cc_final: 0.8218 (m-80) REVERT: A 748 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6882 (tm-30) REVERT: A 749 MET cc_start: 0.7285 (mtt) cc_final: 0.6563 (mtt) REVERT: A 998 ILE cc_start: 0.9392 (mt) cc_final: 0.9159 (tt) REVERT: A 1029 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8323 (tp30) REVERT: A 1064 ASP cc_start: 0.8659 (t0) cc_final: 0.8421 (t0) REVERT: A 1068 ILE cc_start: 0.9445 (mt) cc_final: 0.9160 (mm) REVERT: A 1091 ASN cc_start: 0.7660 (t0) cc_final: 0.6709 (t0) REVERT: D 68 TYR cc_start: 0.8434 (m-80) cc_final: 0.7417 (m-80) REVERT: D 75 ILE cc_start: 0.8209 (mt) cc_final: 0.7870 (mm) REVERT: D 78 GLU cc_start: 0.8219 (pt0) cc_final: 0.7597 (pt0) REVERT: D 110 GLN cc_start: 0.7254 (mt0) cc_final: 0.6855 (mm-40) REVERT: D 111 MET cc_start: 0.7863 (tmm) cc_final: 0.7559 (tmm) REVERT: D 124 MET cc_start: 0.7298 (tmm) cc_final: 0.6829 (tmm) REVERT: B 26 ASN cc_start: 0.8563 (t0) cc_final: 0.7945 (t0) REVERT: B 184 PRO cc_start: 0.8542 (Cg_exo) cc_final: 0.8282 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8856 (mt) cc_final: 0.8589 (mt) REVERT: B 643 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8108 (m-70) REVERT: B 694 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 749 MET cc_start: 0.7455 (mtt) cc_final: 0.7231 (mtt) REVERT: B 940 TRP cc_start: 0.7001 (t-100) cc_final: 0.6775 (t-100) REVERT: B 1029 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 1064 ASP cc_start: 0.8658 (t0) cc_final: 0.8449 (t0) REVERT: B 1091 ASN cc_start: 0.7538 (t0) cc_final: 0.6610 (t0) REVERT: E 88 MET cc_start: 0.8812 (ttp) cc_final: 0.8564 (ttp) REVERT: E 91 THR cc_start: 0.8535 (p) cc_final: 0.8314 (p) REVERT: E 110 GLN cc_start: 0.7271 (mt0) cc_final: 0.6717 (mm-40) REVERT: E 111 MET cc_start: 0.7639 (tmm) cc_final: 0.7401 (tmm) REVERT: E 124 MET cc_start: 0.7129 (tmm) cc_final: 0.6802 (tmm) REVERT: C 26 ASN cc_start: 0.8531 (t0) cc_final: 0.8066 (t0) REVERT: C 184 PRO cc_start: 0.8603 (Cg_exo) cc_final: 0.8297 (Cg_endo) REVERT: C 410 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: C 735 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7946 (pp) REVERT: C 748 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6766 (tm-30) REVERT: C 814 MET cc_start: 0.8921 (mmp) cc_final: 0.8599 (tpp) REVERT: C 940 TRP cc_start: 0.6926 (t-100) cc_final: 0.6446 (t-100) REVERT: C 1064 ASP cc_start: 0.8638 (t0) cc_final: 0.8384 (t0) REVERT: C 1068 ILE cc_start: 0.9415 (mm) cc_final: 0.9187 (mm) REVERT: C 1086 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8303 (pp30) REVERT: C 1091 ASN cc_start: 0.7892 (t0) cc_final: 0.6996 (t0) REVERT: C 1111 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8581 (p90) REVERT: F 110 GLN cc_start: 0.7432 (mt0) cc_final: 0.6738 (mm-40) REVERT: F 111 MET cc_start: 0.7745 (tmm) cc_final: 0.7486 (tmm) outliers start: 140 outliers final: 108 residues processed: 394 average time/residue: 0.3692 time to fit residues: 244.6914 Evaluate side-chains 381 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 267 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 410 PHE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 706 CYS Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1086 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 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: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 469 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN ** A1091 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** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 ASN ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** 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** ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29394 Z= 0.240 Angle : 0.612 9.762 40032 Z= 0.326 Chirality : 0.044 0.198 4536 Planarity : 0.004 0.054 5208 Dihedral : 6.619 59.285 4273 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.38 % Allowed : 20.54 % Favored : 75.08 % 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: -2.54 (0.13), residues: 3663 helix: -0.33 (0.19), residues: 744 sheet: -1.98 (0.19), residues: 651 loop : -2.15 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 940 HIS 0.006 0.001 HIS B 506 PHE 0.015 0.001 PHE A 393 TYR 0.017 0.001 TYR B1111 ARG 0.003 0.000 ARG C 867 *********************** 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 428 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 290 time to evaluate : 3.277 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: A 137 TYR cc_start: 0.8607 (m-80) cc_final: 0.8345 (m-10) REVERT: A 184 PRO cc_start: 0.8540 (Cg_exo) cc_final: 0.8334 (Cg_endo) REVERT: A 358 LEU cc_start: 0.8427 (mm) cc_final: 0.8223 (tt) REVERT: A 642 PHE cc_start: 0.8454 (m-80) cc_final: 0.8166 (m-80) REVERT: A 749 MET cc_start: 0.7309 (mtt) cc_final: 0.6853 (mtt) REVERT: A 998 ILE cc_start: 0.9327 (mt) cc_final: 0.9096 (tt) REVERT: A 1018 ASN cc_start: 0.7652 (t0) cc_final: 0.7383 (t0) REVERT: A 1029 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8245 (tp30) REVERT: A 1064 ASP cc_start: 0.8650 (t0) cc_final: 0.8333 (t0) REVERT: A 1068 ILE cc_start: 0.9447 (mt) cc_final: 0.9075 (mm) REVERT: A 1091 ASN cc_start: 0.7657 (t0) cc_final: 0.6664 (t0) REVERT: D 68 TYR cc_start: 0.8418 (m-80) cc_final: 0.7882 (m-80) REVERT: D 78 GLU cc_start: 0.8200 (pt0) cc_final: 0.7893 (pt0) REVERT: D 110 GLN cc_start: 0.7251 (mt0) cc_final: 0.6864 (mm-40) REVERT: D 111 MET cc_start: 0.7881 (tmm) cc_final: 0.7572 (tmm) REVERT: D 124 MET cc_start: 0.7380 (tmm) cc_final: 0.6943 (tmm) REVERT: B 26 ASN cc_start: 0.8535 (t0) cc_final: 0.7944 (t0) REVERT: B 184 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8273 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8812 (mt) cc_final: 0.8526 (mt) REVERT: B 643 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.7934 (m-70) REVERT: B 668 ARG cc_start: 0.7526 (ptm-80) cc_final: 0.7010 (ptt90) REVERT: B 694 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8518 (mp) REVERT: B 940 TRP cc_start: 0.6913 (t-100) cc_final: 0.6685 (t-100) REVERT: B 1029 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 1064 ASP cc_start: 0.8625 (t0) cc_final: 0.8374 (t0) REVERT: B 1091 ASN cc_start: 0.7539 (t0) cc_final: 0.6595 (t0) REVERT: E 91 THR cc_start: 0.8479 (p) cc_final: 0.8263 (p) REVERT: E 110 GLN cc_start: 0.7310 (mt0) cc_final: 0.6679 (mm-40) REVERT: E 111 MET cc_start: 0.7613 (tmm) cc_final: 0.7363 (tmm) REVERT: E 124 MET cc_start: 0.7021 (tmm) cc_final: 0.6714 (tmm) REVERT: C 26 ASN cc_start: 0.8558 (t0) cc_final: 0.8065 (t0) REVERT: C 184 PRO cc_start: 0.8612 (Cg_exo) cc_final: 0.8343 (Cg_endo) REVERT: C 694 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8532 (mp) REVERT: C 735 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7863 (pp) REVERT: C 748 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6751 (tm-30) REVERT: C 814 MET cc_start: 0.8920 (mmp) cc_final: 0.8610 (tpp) REVERT: C 940 TRP cc_start: 0.6814 (t-100) cc_final: 0.6402 (t-100) REVERT: C 1064 ASP cc_start: 0.8599 (t0) cc_final: 0.8347 (t0) REVERT: C 1068 ILE cc_start: 0.9431 (mm) cc_final: 0.9191 (mm) REVERT: C 1091 ASN cc_start: 0.7913 (t0) cc_final: 0.6972 (t0) REVERT: C 1111 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8587 (p90) REVERT: F 36 VAL cc_start: 0.7123 (m) cc_final: 0.6879 (m) REVERT: F 111 MET cc_start: 0.7732 (tmm) cc_final: 0.7463 (tmm) outliers start: 138 outliers final: 109 residues processed: 392 average time/residue: 0.3582 time to fit residues: 235.3986 Evaluate side-chains 381 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 267 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 964 ASN Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 706 CYS Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 20.0000 chunk 318 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 523 HIS A 643 HIS ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN A1018 ASN ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 325 ASN B 428 HIS B 643 HIS ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 314 GLN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 HIS C 469 GLN C 556 ASN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 29394 Z= 0.495 Angle : 0.763 10.734 40032 Z= 0.405 Chirality : 0.047 0.224 4536 Planarity : 0.005 0.051 5208 Dihedral : 7.010 59.967 4273 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 6.03 % Allowed : 20.13 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.75 (0.13), residues: 3663 helix: -0.33 (0.19), residues: 732 sheet: -2.19 (0.19), residues: 654 loop : -2.33 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 940 HIS 0.007 0.002 HIS A 205 PHE 0.029 0.002 PHE A 393 TYR 0.024 0.002 TYR B 207 ARG 0.006 0.001 ARG A 399 *********************** 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 452 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 262 time to evaluate : 3.144 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: A 134 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6726 (p90) REVERT: A 321 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7191 (ttm-80) REVERT: A 358 LEU cc_start: 0.8469 (mm) cc_final: 0.8123 (tt) REVERT: A 637 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6675 (ptt180) REVERT: A 642 PHE cc_start: 0.8712 (m-80) cc_final: 0.8393 (m-80) REVERT: A 749 MET cc_start: 0.7469 (mtt) cc_final: 0.7119 (mtt) REVERT: A 1029 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8283 (tp30) REVERT: A 1064 ASP cc_start: 0.8719 (t0) cc_final: 0.8372 (t0) REVERT: A 1068 ILE cc_start: 0.9479 (mt) cc_final: 0.9086 (mm) REVERT: A 1091 ASN cc_start: 0.7894 (t0) cc_final: 0.6873 (t0) REVERT: A 1166 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.8006 (tp) REVERT: D 68 TYR cc_start: 0.8604 (m-80) cc_final: 0.8080 (m-80) REVERT: D 78 GLU cc_start: 0.8342 (pt0) cc_final: 0.8045 (pt0) REVERT: D 110 GLN cc_start: 0.7366 (mt0) cc_final: 0.6863 (mm-40) REVERT: D 111 MET cc_start: 0.7927 (tmm) cc_final: 0.7645 (tmm) REVERT: D 124 MET cc_start: 0.7355 (tmm) cc_final: 0.7055 (tmm) REVERT: B 26 ASN cc_start: 0.8574 (t0) cc_final: 0.8001 (t0) REVERT: B 134 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7469 (p90) REVERT: B 184 PRO cc_start: 0.8533 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: B 321 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7743 (ttm-80) REVERT: B 431 LEU cc_start: 0.8919 (mt) cc_final: 0.8604 (mt) REVERT: B 643 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.7694 (m90) REVERT: B 694 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8542 (mt) REVERT: B 804 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8629 (mm) REVERT: B 940 TRP cc_start: 0.7343 (t-100) cc_final: 0.7044 (t-100) REVERT: B 1029 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 1064 ASP cc_start: 0.8697 (t0) cc_final: 0.8442 (t0) REVERT: B 1091 ASN cc_start: 0.7773 (t0) cc_final: 0.6864 (t0) REVERT: E 111 MET cc_start: 0.7642 (tmm) cc_final: 0.7359 (tmm) REVERT: E 124 MET cc_start: 0.7247 (tmm) cc_final: 0.7037 (tmm) REVERT: C 134 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6906 (p90) REVERT: C 321 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7674 (ttm-80) REVERT: C 643 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.7671 (m90) REVERT: C 694 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8522 (mt) REVERT: C 701 MET cc_start: 0.7867 (ttp) cc_final: 0.7570 (ptm) REVERT: C 735 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8057 (pp) REVERT: C 814 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8673 (tpp) REVERT: C 940 TRP cc_start: 0.7060 (t-100) cc_final: 0.6605 (t-100) REVERT: C 1064 ASP cc_start: 0.8590 (t0) cc_final: 0.8269 (t0) REVERT: C 1068 ILE cc_start: 0.9468 (mm) cc_final: 0.9184 (mm) REVERT: C 1091 ASN cc_start: 0.8117 (t0) cc_final: 0.7183 (t0) REVERT: C 1111 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8647 (p90) REVERT: F 36 VAL cc_start: 0.7023 (m) cc_final: 0.6723 (m) REVERT: F 111 MET cc_start: 0.7742 (tmm) cc_final: 0.7499 (tmm) outliers start: 190 outliers final: 130 residues processed: 421 average time/residue: 0.3747 time to fit residues: 260.4725 Evaluate side-chains 394 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 248 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 706 CYS Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1128 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 352 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 GLN A 964 ASN A1018 ASN ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN C 556 ASN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN C 964 ASN C1018 ASN ** C1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29394 Z= 0.189 Angle : 0.612 10.078 40032 Z= 0.325 Chirality : 0.044 0.199 4536 Planarity : 0.004 0.055 5208 Dihedral : 6.548 59.304 4273 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.41 % Allowed : 22.19 % Favored : 73.40 % 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: -2.54 (0.13), residues: 3663 helix: -0.19 (0.19), residues: 753 sheet: -2.03 (0.19), residues: 648 loop : -2.20 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 346 HIS 0.011 0.001 HIS A 643 PHE 0.014 0.001 PHE C 550 TYR 0.017 0.001 TYR A1111 ARG 0.003 0.000 ARG B 867 *********************** 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 423 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 284 time to evaluate : 3.435 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: A 358 LEU cc_start: 0.8424 (mm) cc_final: 0.8188 (tt) REVERT: A 637 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6593 (ptt180) REVERT: A 643 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7673 (m-70) REVERT: A 749 MET cc_start: 0.7375 (mtt) cc_final: 0.6849 (mtt) REVERT: A 998 ILE cc_start: 0.9295 (mt) cc_final: 0.9061 (tt) REVERT: A 1029 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8143 (tp30) REVERT: A 1064 ASP cc_start: 0.8685 (t0) cc_final: 0.8417 (t0) REVERT: A 1068 ILE cc_start: 0.9446 (mt) cc_final: 0.9127 (mm) REVERT: A 1091 ASN cc_start: 0.7700 (t0) cc_final: 0.6784 (t0) REVERT: D 68 TYR cc_start: 0.8503 (m-80) cc_final: 0.7996 (m-80) REVERT: D 78 GLU cc_start: 0.8303 (pt0) cc_final: 0.8039 (pt0) REVERT: D 88 MET cc_start: 0.8759 (ttp) cc_final: 0.7847 (tmm) REVERT: D 110 GLN cc_start: 0.7274 (mt0) cc_final: 0.6751 (mm-40) REVERT: D 111 MET cc_start: 0.7952 (tmm) cc_final: 0.7674 (tmm) REVERT: D 124 MET cc_start: 0.7383 (tmm) cc_final: 0.6839 (tmm) REVERT: B 184 PRO cc_start: 0.8517 (Cg_exo) cc_final: 0.8295 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8833 (mt) cc_final: 0.8579 (mt) REVERT: B 643 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7406 (m-70) REVERT: B 940 TRP cc_start: 0.6977 (t-100) cc_final: 0.6440 (t-100) REVERT: B 1029 GLU cc_start: 0.8242 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 1091 ASN cc_start: 0.7577 (t0) cc_final: 0.6622 (t0) REVERT: E 111 MET cc_start: 0.7639 (tmm) cc_final: 0.7345 (tmm) REVERT: C 26 ASN cc_start: 0.8619 (t0) cc_final: 0.8147 (t0) REVERT: C 184 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8217 (Cg_endo) REVERT: C 735 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7849 (pp) REVERT: C 748 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6773 (tm-30) REVERT: C 814 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8610 (tpp) REVERT: C 998 ILE cc_start: 0.9352 (mt) cc_final: 0.9018 (tt) REVERT: C 1064 ASP cc_start: 0.8598 (t0) cc_final: 0.8306 (t0) REVERT: C 1068 ILE cc_start: 0.9412 (mm) cc_final: 0.9125 (mm) REVERT: C 1091 ASN cc_start: 0.7914 (t0) cc_final: 0.7021 (t0) REVERT: C 1111 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8694 (p90) REVERT: F 111 MET cc_start: 0.7778 (tmm) cc_final: 0.7532 (tmm) REVERT: F 124 MET cc_start: 0.6831 (tmm) cc_final: 0.6537 (tmm) outliers start: 139 outliers final: 109 residues processed: 390 average time/residue: 0.3772 time to fit residues: 245.9246 Evaluate side-chains 372 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 257 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 964 ASN Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1018 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 964 ASN Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1018 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1063 SER Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 121 THR 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: 8.9990 chunk 210 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 68 optimal weight: 0.6980 chunk 224 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 GLN A 765 GLN A 964 ASN A1018 ASN ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 ASN C1018 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29394 Z= 0.243 Angle : 0.622 11.804 40032 Z= 0.331 Chirality : 0.045 0.191 4536 Planarity : 0.004 0.052 5208 Dihedral : 6.438 57.539 4271 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.83 % Allowed : 22.16 % Favored : 73.02 % 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: -2.45 (0.13), residues: 3663 helix: 0.09 (0.19), residues: 726 sheet: -2.01 (0.19), residues: 651 loop : -2.19 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 940 HIS 0.004 0.001 HIS B 643 PHE 0.031 0.001 PHE E 90 TYR 0.020 0.001 TYR A1111 ARG 0.005 0.000 ARG C 867 *********************** 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 415 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 263 time to evaluate : 3.257 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: A 358 LEU cc_start: 0.8443 (mm) cc_final: 0.8161 (tt) REVERT: A 637 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6603 (ptt180) REVERT: A 643 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7626 (m-70) REVERT: A 749 MET cc_start: 0.7448 (mtt) cc_final: 0.6906 (mtt) REVERT: A 940 TRP cc_start: 0.7143 (t-100) cc_final: 0.6746 (t-100) REVERT: A 998 ILE cc_start: 0.9324 (mt) cc_final: 0.9072 (tt) REVERT: A 1068 ILE cc_start: 0.9471 (mt) cc_final: 0.9162 (mm) REVERT: A 1091 ASN cc_start: 0.7814 (t0) cc_final: 0.6893 (t0) REVERT: D 68 TYR cc_start: 0.8544 (m-80) cc_final: 0.8031 (m-80) REVERT: D 78 GLU cc_start: 0.8305 (pt0) cc_final: 0.8024 (pt0) REVERT: D 88 MET cc_start: 0.8749 (ttp) cc_final: 0.7688 (tmm) REVERT: D 110 GLN cc_start: 0.7270 (mt0) cc_final: 0.6716 (mm-40) REVERT: D 111 MET cc_start: 0.7957 (tmm) cc_final: 0.7680 (tmm) REVERT: D 124 MET cc_start: 0.7409 (tmm) cc_final: 0.6826 (tmm) REVERT: B 184 PRO cc_start: 0.8504 (Cg_exo) cc_final: 0.8283 (Cg_endo) REVERT: B 321 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7674 (ttm-80) REVERT: B 431 LEU cc_start: 0.8818 (mt) cc_final: 0.8549 (mt) REVERT: B 643 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.7469 (m-70) REVERT: B 749 MET cc_start: 0.7593 (mtt) cc_final: 0.7272 (mtm) REVERT: B 940 TRP cc_start: 0.6896 (t-100) cc_final: 0.6578 (t-100) REVERT: B 1029 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8042 (tm-30) REVERT: B 1091 ASN cc_start: 0.7577 (t0) cc_final: 0.6606 (t0) REVERT: E 90 PHE cc_start: 0.8175 (m-80) cc_final: 0.7655 (m-10) REVERT: E 111 MET cc_start: 0.7684 (tmm) cc_final: 0.7378 (tmm) REVERT: C 26 ASN cc_start: 0.8561 (t0) cc_final: 0.8083 (t0) REVERT: C 184 PRO cc_start: 0.8462 (Cg_exo) cc_final: 0.8203 (Cg_endo) REVERT: C 643 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.7441 (m90) REVERT: C 735 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7907 (pp) REVERT: C 748 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6812 (tm-30) REVERT: C 814 MET cc_start: 0.8934 (mmp) cc_final: 0.8613 (tpp) REVERT: C 1064 ASP cc_start: 0.8610 (t0) cc_final: 0.8290 (t0) REVERT: C 1068 ILE cc_start: 0.9421 (mm) cc_final: 0.9135 (mm) REVERT: C 1091 ASN cc_start: 0.7959 (t0) cc_final: 0.7058 (t0) REVERT: C 1111 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8641 (p90) REVERT: F 75 ILE cc_start: 0.8178 (mt) cc_final: 0.7858 (mm) REVERT: F 111 MET cc_start: 0.7742 (tmm) cc_final: 0.7495 (tmm) REVERT: F 124 MET cc_start: 0.6851 (tmm) cc_final: 0.6523 (tmm) outliers start: 152 outliers final: 126 residues processed: 386 average time/residue: 0.3531 time to fit residues: 229.6539 Evaluate side-chains 377 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 244 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 964 ASN Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1018 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 706 CYS Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1018 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 121 THR 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: 0.9990 chunk 308 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 ASN C1018 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29394 Z= 0.301 Angle : 0.650 10.036 40032 Z= 0.345 Chirality : 0.045 0.188 4536 Planarity : 0.005 0.144 5208 Dihedral : 6.482 56.543 4271 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.95 % Allowed : 22.60 % Favored : 72.44 % 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: -2.44 (0.13), residues: 3663 helix: 0.13 (0.19), residues: 726 sheet: -1.93 (0.19), residues: 666 loop : -2.23 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 940 HIS 0.005 0.001 HIS D 56 PHE 0.023 0.002 PHE D 90 TYR 0.019 0.002 TYR A1111 ARG 0.006 0.000 ARG C 867 *********************** 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 409 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 253 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 LEU cc_start: 0.8417 (mm) cc_final: 0.8092 (tt) REVERT: A 637 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6735 (ptt180) REVERT: A 749 MET cc_start: 0.7493 (mtt) cc_final: 0.6930 (mtt) REVERT: A 814 MET cc_start: 0.8840 (mmp) cc_final: 0.8556 (tpp) REVERT: A 823 MET cc_start: 0.7691 (ttp) cc_final: 0.7338 (ttp) REVERT: A 940 TRP cc_start: 0.7209 (t-100) cc_final: 0.6892 (t-100) REVERT: A 998 ILE cc_start: 0.9335 (mt) cc_final: 0.9087 (tt) REVERT: A 1064 ASP cc_start: 0.8478 (t0) cc_final: 0.8245 (t0) REVERT: A 1068 ILE cc_start: 0.9489 (mt) cc_final: 0.9255 (mm) REVERT: A 1091 ASN cc_start: 0.7797 (t0) cc_final: 0.6899 (t0) REVERT: D 68 TYR cc_start: 0.8568 (m-80) cc_final: 0.8011 (m-80) REVERT: D 78 GLU cc_start: 0.8323 (pt0) cc_final: 0.8025 (pt0) REVERT: D 88 MET cc_start: 0.8711 (ttp) cc_final: 0.7707 (tmm) REVERT: D 110 GLN cc_start: 0.7296 (mt0) cc_final: 0.6664 (mm-40) REVERT: D 111 MET cc_start: 0.7956 (tmm) cc_final: 0.7681 (tmm) REVERT: D 124 MET cc_start: 0.7472 (tmm) cc_final: 0.6900 (tmm) REVERT: B 134 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7500 (p90) REVERT: B 321 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7718 (ttm-80) REVERT: B 431 LEU cc_start: 0.8827 (mt) cc_final: 0.8550 (mt) REVERT: B 643 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.7524 (m-70) REVERT: B 749 MET cc_start: 0.7565 (mtt) cc_final: 0.7059 (mtm) REVERT: B 940 TRP cc_start: 0.6991 (t-100) cc_final: 0.6717 (t-100) REVERT: B 1029 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8026 (tm-30) REVERT: B 1091 ASN cc_start: 0.7646 (t0) cc_final: 0.6769 (t0) REVERT: E 90 PHE cc_start: 0.8219 (m-80) cc_final: 0.7733 (m-10) REVERT: E 111 MET cc_start: 0.7682 (tmm) cc_final: 0.7383 (tmm) REVERT: C 633 CYS cc_start: 0.4862 (m) cc_final: 0.4612 (m) REVERT: C 643 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7500 (m90) REVERT: C 735 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7973 (pp) REVERT: C 814 MET cc_start: 0.8968 (mmp) cc_final: 0.8636 (tpp) REVERT: C 1064 ASP cc_start: 0.8629 (t0) cc_final: 0.8300 (t0) REVERT: C 1068 ILE cc_start: 0.9411 (mm) cc_final: 0.9115 (mm) REVERT: C 1091 ASN cc_start: 0.7994 (t0) cc_final: 0.7075 (t0) REVERT: C 1111 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8583 (p90) REVERT: F 75 ILE cc_start: 0.8213 (mt) cc_final: 0.7756 (mm) REVERT: F 111 MET cc_start: 0.7735 (tmm) cc_final: 0.7483 (tmm) REVERT: F 124 MET cc_start: 0.6845 (tmm) cc_final: 0.6534 (tmm) outliers start: 156 outliers final: 136 residues processed: 379 average time/residue: 0.3590 time to fit residues: 228.5043 Evaluate side-chains 384 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 241 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 706 CYS Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 964 ASN Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1018 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 0.9980 chunk 347 optimal weight: 0.9990 chunk 212 optimal weight: 0.3980 chunk 164 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 364 optimal weight: 9.9990 chunk 335 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 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 172 ASN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS C 172 ASN C 643 HIS ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 ASN C1018 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29394 Z= 0.170 Angle : 0.615 9.608 40032 Z= 0.324 Chirality : 0.044 0.200 4536 Planarity : 0.004 0.100 5208 Dihedral : 6.251 59.226 4271 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.13 % Allowed : 23.59 % Favored : 72.29 % 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: -2.24 (0.13), residues: 3663 helix: 0.23 (0.19), residues: 747 sheet: -1.71 (0.19), residues: 660 loop : -2.12 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 940 HIS 0.005 0.001 HIS D 56 PHE 0.051 0.001 PHE D 90 TYR 0.025 0.001 TYR F 68 ARG 0.007 0.000 ARG C 867 ********************** 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 409 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 279 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 ASN cc_start: 0.8992 (p0) cc_final: 0.8780 (p0) REVERT: A 633 CYS cc_start: 0.4817 (m) cc_final: 0.4601 (m) REVERT: A 643 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7600 (m-70) REVERT: A 749 MET cc_start: 0.7371 (mtt) cc_final: 0.6814 (mtt) REVERT: A 867 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7703 (ptp-170) REVERT: A 940 TRP cc_start: 0.7037 (t-100) cc_final: 0.6757 (t-100) REVERT: A 998 ILE cc_start: 0.9276 (mt) cc_final: 0.9031 (tt) REVERT: A 1064 ASP cc_start: 0.8461 (t0) cc_final: 0.8220 (t0) REVERT: A 1068 ILE cc_start: 0.9468 (mt) cc_final: 0.9222 (mm) REVERT: A 1091 ASN cc_start: 0.7717 (t0) cc_final: 0.6789 (t0) REVERT: D 68 TYR cc_start: 0.8425 (m-80) cc_final: 0.7919 (m-80) REVERT: D 78 GLU cc_start: 0.8292 (pt0) cc_final: 0.7988 (pt0) REVERT: D 88 MET cc_start: 0.8617 (ttp) cc_final: 0.7701 (tmm) REVERT: D 111 MET cc_start: 0.7971 (tmm) cc_final: 0.7665 (tmm) REVERT: D 124 MET cc_start: 0.7502 (tmm) cc_final: 0.6919 (tmm) REVERT: B 149 MET cc_start: 0.8141 (pmm) cc_final: 0.7891 (pmm) REVERT: B 321 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7460 (ttm-80) REVERT: B 431 LEU cc_start: 0.8837 (mt) cc_final: 0.8623 (mt) REVERT: B 643 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7318 (m-70) REVERT: B 701 MET cc_start: 0.7529 (ttp) cc_final: 0.7321 (ptp) REVERT: B 749 MET cc_start: 0.7526 (mtt) cc_final: 0.6992 (mtm) REVERT: B 940 TRP cc_start: 0.6657 (t-100) cc_final: 0.6350 (t-100) REVERT: B 1029 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 1090 ILE cc_start: 0.8683 (mt) cc_final: 0.8450 (mt) REVERT: B 1091 ASN cc_start: 0.7554 (t0) cc_final: 0.6534 (t0) REVERT: E 90 PHE cc_start: 0.8090 (m-80) cc_final: 0.7628 (m-80) REVERT: E 111 MET cc_start: 0.7675 (tmm) cc_final: 0.7384 (tmm) REVERT: E 124 MET cc_start: 0.6813 (tmm) cc_final: 0.6234 (tmm) REVERT: C 643 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7577 (m-70) REVERT: C 735 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7845 (pp) REVERT: C 867 ARG cc_start: 0.8170 (ptp-170) cc_final: 0.7875 (ptp-170) REVERT: C 998 ILE cc_start: 0.9267 (mt) cc_final: 0.8990 (tt) REVERT: C 1029 GLU cc_start: 0.8679 (tp30) cc_final: 0.8441 (tp30) REVERT: C 1064 ASP cc_start: 0.8608 (t0) cc_final: 0.8352 (t0) REVERT: C 1068 ILE cc_start: 0.9345 (mm) cc_final: 0.9073 (mm) REVERT: C 1091 ASN cc_start: 0.7848 (t0) cc_final: 0.6955 (t0) REVERT: C 1111 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8607 (p90) REVERT: F 90 PHE cc_start: 0.8527 (m-80) cc_final: 0.8025 (m-80) REVERT: F 111 MET cc_start: 0.7751 (tmm) cc_final: 0.7482 (tmm) REVERT: F 124 MET cc_start: 0.6651 (tmm) cc_final: 0.6366 (tmm) outliers start: 130 outliers final: 110 residues processed: 381 average time/residue: 0.3530 time to fit residues: 226.8590 Evaluate side-chains 376 residues out of total 3159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 260 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain D residue 56 HIS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 783 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 964 ASN Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 290 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 428 HIS ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN D 110 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 ASN C1018 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.088536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071837 restraints weight = 87574.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.074142 restraints weight = 51347.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075766 restraints weight = 35487.624| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29394 Z= 0.205 Angle : 0.622 12.399 40032 Z= 0.325 Chirality : 0.044 0.196 4536 Planarity : 0.004 0.091 5208 Dihedral : 6.198 58.456 4271 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.16 % Allowed : 23.56 % Favored : 72.29 % 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: -2.10 (0.14), residues: 3663 helix: 0.41 (0.20), residues: 729 sheet: -1.49 (0.20), residues: 606 loop : -2.07 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 940 HIS 0.014 0.001 HIS C 643 PHE 0.043 0.001 PHE D 90 TYR 0.023 0.001 TYR F 120 ARG 0.008 0.000 ARG C 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5491.14 seconds wall clock time: 101 minutes 52.72 seconds (6112.72 seconds total)