Starting phenix.real_space_refine on Fri Jun 20 05:48:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzn_22534/06_2025/7jzn_22534.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzn_22534/06_2025/7jzn_22534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzn_22534/06_2025/7jzn_22534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzn_22534/06_2025/7jzn_22534.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzn_22534/06_2025/7jzn_22534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzn_22534/06_2025/7jzn_22534.cif" } resolution = 3.1 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= 0.004 sd= 0.062 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 102 5.16 5 C 14846 2.51 5 N 3902 2.21 5 O 4458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23308 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7360 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 52, 'TRANS': 924} Chain breaks: 11 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 165 Chain: "E" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 320 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 132 Chain: "B" Number of atoms: 7187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7187 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 52, 'TRANS': 924} Chain breaks: 10 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 285 Chain: "F" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 320 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 6975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 6975 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 52, 'TRANS': 933} Chain breaks: 9 Unresolved non-hydrogen bonds: 758 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 1, 'ASP:plan': 25, 'PHE:plan': 13, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 453 Chain: "G" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 320 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 132 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.79, per 1000 atoms: 0.63 Number of scatterers: 23308 At special positions: 0 Unit cell: (130.2, 130.2, 198.45, 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 102 16.00 O 4458 8.00 N 3902 7.00 C 14846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.10 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.11 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.08 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.28 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.10 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.07 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.71 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.07 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 2.9 seconds 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5892 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 44 sheets defined 30.2% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.918A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.410A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.673A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.616A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.155A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.543A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.609A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.970A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.783A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'E' and resid 22 through 42 removed outlier: 3.593A pdb=" N LYS E 26 " --> pdb=" O ASP E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 64 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.609A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.651A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.958A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.090A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.689A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.922A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'F' and resid 22 through 42 removed outlier: 3.502A pdb=" N LYS F 26 " --> pdb=" O ASP F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 64 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.766A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.781A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.829A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 890 removed outlier: 4.181A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.504A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.583A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 945 Processing helix chain 'C' and resid 946 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.068A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1145 Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'G' and resid 22 through 42 Processing helix chain 'G' and resid 44 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.072A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.946A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.408A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.598A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.356A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.950A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.410A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.314A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.828A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.388A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 4.065A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.810A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.103A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.646A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.220A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.282A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.282A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.634A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.436A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.689A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.931A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.112A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.766A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.126A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.278A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.354A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.370A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.619A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.346A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.901A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.732A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1155 hydrogen bonds defined for protein. 3192 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: 10.30 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6520 1.33 - 1.47: 6986 1.47 - 1.61: 10140 1.61 - 1.75: 3 1.75 - 1.88: 126 Bond restraints: 23775 Sorted by residual: bond pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 1.530 1.616 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C ASN B 81 " pdb=" N PRO B 82 " ideal model delta sigma weight residual 1.329 1.377 -0.049 1.20e-02 6.94e+03 1.65e+01 bond pdb=" CB LEU A 110 " pdb=" CG LEU A 110 " ideal model delta sigma weight residual 1.530 1.611 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" CB LEU B 216 " pdb=" CG LEU B 216 " ideal model delta sigma weight residual 1.530 1.611 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" CG PHE A 855 " pdb=" CD2 PHE A 855 " ideal model delta sigma weight residual 1.384 1.459 -0.075 2.10e-02 2.27e+03 1.28e+01 ... (remaining 23770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 31996 4.40 - 8.79: 496 8.79 - 13.19: 5 13.19 - 17.59: 0 17.59 - 21.98: 5 Bond angle restraints: 32502 Sorted by residual: angle pdb=" N ALA A1070 " pdb=" CA ALA A1070 " pdb=" C ALA A1070 " ideal model delta sigma weight residual 111.96 133.94 -21.98 1.41e+00 5.03e-01 2.43e+02 angle pdb=" N GLN A1071 " pdb=" CA GLN A1071 " pdb=" CB GLN A1071 " ideal model delta sigma weight residual 110.81 129.83 -19.02 1.68e+00 3.54e-01 1.28e+02 angle pdb=" N GLN A1071 " pdb=" CA GLN A1071 " pdb=" C GLN A1071 " ideal model delta sigma weight residual 108.69 88.79 19.90 1.77e+00 3.19e-01 1.26e+02 angle pdb=" CD1 LEU B1034 " pdb=" CG LEU B1034 " pdb=" CD2 LEU B1034 " ideal model delta sigma weight residual 110.80 91.92 18.88 2.20e+00 2.07e-01 7.37e+01 angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 125.05 -5.39 7.20e-01 1.93e+00 5.61e+01 ... (remaining 32497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 14301 17.83 - 35.67: 432 35.67 - 53.50: 78 53.50 - 71.33: 38 71.33 - 89.17: 22 Dihedral angle restraints: 14871 sinusoidal: 5772 harmonic: 9099 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.39 66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 146.05 -53.05 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 47.51 45.49 1 1.00e+01 1.00e-02 2.87e+01 ... (remaining 14868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 3643 0.148 - 0.296: 295 0.296 - 0.444: 67 0.444 - 0.592: 0 0.592 - 0.740: 3 Chirality restraints: 4008 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.95e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.13e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.96e+01 ... (remaining 4005 not shown) Planarity restraints: 4212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.053 2.00e-02 2.50e+03 5.55e-02 3.85e+01 pdb=" CG ASN C 234 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " -0.043 2.00e-02 2.50e+03 4.39e-02 2.41e+01 pdb=" CG ASN C 603 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.042 2.00e-02 2.50e+03 4.32e-02 2.33e+01 pdb=" CG ASN A 603 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " 0.066 2.00e-02 2.50e+03 pdb=" C1 NAG A1307 " -0.052 2.00e-02 2.50e+03 ... (remaining 4209 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7969 2.86 - 3.37: 20965 3.37 - 3.88: 39014 3.88 - 4.39: 44095 4.39 - 4.90: 73932 Nonbonded interactions: 185975 Sorted by model distance: nonbonded pdb=" NZ LYS B 557 " pdb=" OD2 ASP B 574 " model vdw 2.353 3.120 nonbonded pdb=" N GLN A1071 " pdb=" O GLN A1071 " model vdw 2.417 2.496 nonbonded pdb=" N ASP A1084 " pdb=" OD1 ASP A1084 " model vdw 2.432 3.120 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.440 3.120 nonbonded pdb=" O GLY B 601 " pdb=" N THR B 604 " model vdw 2.448 3.120 ... (remaining 185970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 44 or (resid 45 through 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 59 or (res \ id 60 and (name N or name CA or name C or name O or name CB )) or resid 61 throu \ gh 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) or r \ esid 64 through 65 or (resid 66 and (name N or name CA or name C or name O or na \ me CB )) or resid 82 through 87 or (resid 88 and (name N or name CA or name C or \ name O or name CB )) or resid 89 through 101 or (resid 102 and (name N or name \ CA or name C or name O or name CB )) or resid 103 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 119 or \ (resid 120 through 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 through 123 or (resid 124 through 127 and (name N or name CA or na \ me C or name O or name CB )) or resid 128 or (resid 129 through 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 through 139 or (resid \ 140 and (name N or name CA or name C or name O or name CB )) or resid 166 throug \ h 167 or (resid 168 through 172 and (name N or name CA or name C or name O or na \ me CB )) or resid 188 through 196 or resid 200 through 204 or (resid 205 and (na \ me N or name CA or name C or name O or name CB )) or resid 206 through 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 216 t \ hrough 227 or (resid 228 and (name N or name CA or name C or name O or name CB ) \ ) or resid 229 through 235 or (resid 236 and (name N or name CA or name C or nam \ e O or name CB )) or resid 237 through 238 or (resid 239 through 240 and (name N \ or name CA or name C or name O or name CB )) or resid 241 through 286 or (resid \ 287 through 288 and (name N or name CA or name C or name O or name CB )) or res \ id 289 through 304 or (resid 305 and (name N or name CA or name C or name O or n \ ame CB )) or resid 306 through 315 or (resid 316 through 317 and (name N or name \ CA or name C or name O or name CB )) or resid 318 through 322 or (resid 323 thr \ ough 325 and (name N or name CA or name C or name O or name CB )) or resid 326 t \ hrough 331 or (resid 332 through 334 and (name N or name CA or name C or name O \ or name CB )) or resid 335 through 340 or (resid 341 and (name N or name CA or n \ ame C or name O or name CB )) or resid 342 through 345 or (resid 346 through 352 \ and (name N or name CA or name C or name O or name CB )) or resid 353 or (resid \ 354 and (name N or name CA or name C or name O or name CB )) or resid 355 or (r \ esid 356 through 360 and (name N or name CA or name C or name O or name CB )) or \ resid 361 or (resid 362 through 363 and (name N or name CA or name C or name O \ or name CB )) or resid 364 through 366 or (resid 367 through 378 and (name N or \ name CA or name C or name O or name CB )) or resid 379 or (resid 380 and (name N \ or name CA or name C or name O or name CB )) or resid 381 or (resid 382 through \ 383 and (name N or name CA or name C or name O or name CB )) or resid 384 or (r \ esid 385 through 390 and (name N or name CA or name C or name O or name CB )) or \ resid 391 through 393 or (resid 394 and (name N or name CA or name C or name O \ or name CB )) or resid 395 through 397 or (resid 398 through 403 and (name N or \ name CA or name C or name O or name CB )) or (resid 404 through 411 and (name N \ or name CA or name C or name O or name CB )) or resid 412 through 413 or (resid \ 414 through 415 and (name N or name CA or name C or name O or name CB )) or resi \ d 416 or (resid 417 through 425 and (name N or name CA or name C or name O or na \ me CB )) or resid 426 or (resid 427 through 430 and (name N or name CA or name C \ or name O or name CB )) or resid 431 through 432 or (resid 433 through 445 and \ (name N or name CA or name C or name O or name CB )) or (resid 446 through 462 a \ nd (name N or name CA or name C or name O or name CB )) or resid 463 or (resid 4 \ 64 through 475 and (name N or name CA or name C or name O or name CB )) or resid \ 476 through 480 or (resid 481 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 482 through 484 and (name N or name CA or name C or name O or \ name CB )) or resid 485 through 488 or (resid 489 through 490 and (name N or nam \ e CA or name C or name O or name CB )) or resid 491 or (resid 492 through 495 an \ d (name N or name CA or name C or name O or name CB )) or resid 496 or (resid 49 \ 7 through 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 through 504 or (resid 505 through 506 and (name N or name CA or name C or na \ me O or name CB )) or resid 507 or (resid 508 through 520 and (name N or name CA \ or name C or name O or name CB )) or resid 521 through 531 or (resid 532 and (n \ ame N or name CA or name C or name O or name CB )) or resid 533 through 546 or ( \ resid 547 and (name N or name CA or name C or name O or name CB )) or resid 548 \ through 568 or (resid 569 through 572 and (name N or name CA or name C or name O \ or name CB )) or resid 573 through 585 or (resid 586 and (name N or name CA or \ name C or name O or name CB )) or resid 587 through 613 or (resid 614 and (name \ N or name CA or name C or name O or name CB )) or resid 615 through 644 or (resi \ d 645 and (name N or name CA or name C or name O or name CB )) or resid 646 thro \ ugh 674 or (resid 675 through 690 and (name N or name CA or name C or name O or \ name CB )) or resid 691 through 720 or (resid 721 and (name N or name CA or name \ C or name O or name CB )) or resid 722 through 736 or (resid 737 and (name N or \ name CA or name C or name O or name CB )) or resid 738 or (resid 739 and (name \ N or name CA or name C or name O or name CB )) or resid 740 through 746 or (resi \ d 747 through 748 and (name N or name CA or name C or name O or name CB )) or re \ sid 749 through 809 or (resid 810 through 811 and (name N or name CA or name C o \ r name O or name CB )) or (resid 813 and (name N or name CA or name C or name O \ or name CB )) or resid 814 through 827 or (resid 856 and (name N or name CA or n \ ame C or name O or name CB )) or resid 857 through 858 or (resid 859 and (name N \ or name CA or name C or name O or name CB )) or resid 860 through 866 or (resid \ 867 through 868 and (name N or name CA or name C or name O or name CB )) or res \ id 869 through 920 or (resid 921 and (name N or name CA or name C or name O or n \ ame CB )) or resid 922 through 949 or (resid 950 and (name N or name CA or name \ C or name O or name CB )) or resid 951 through 972 or (resid 973 and (name N or \ name CA or name C or name O or name CB )) or resid 974 through 1016 or (resid 10 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 1018 throug \ h 1054 or (resid 1055 through 1056 and (name N or name CA or name C or name O or \ name CB )) or resid 1057 through 1091 or (resid 1092 and (name N or name CA or \ name C or name O or name CB )) or resid 1093 through 1099 or (resid 1100 and (na \ me N or name CA or name C or name O or name CB )) or resid 1101 through 1117 or \ (resid 1118 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 19 through 1144 or (resid 1145 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 44 or (resid 45 through 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 62 or (res \ id 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throu \ gh 66 or resid 82 through 93 or (resid 94 through 100 and (name N or name CA or \ name C or name O or name CB )) or resid 101 through 107 or (resid 108 through 10 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 110 or resid \ 116 through 119 or (resid 120 through 121 and (name N or name CA or name C or n \ ame O or name CB )) or resid 122 through 124 or (resid 125 through 127 and (name \ N or name CA or name C or name O or name CB )) or resid 128 through 129 or (res \ id 130 and (name N or name CA or name C or name O or name CB )) or resid 131 thr \ ough 135 or resid 139 through 166 or (resid 167 through 188 and (name N or name \ CA or name C or name O or name CB )) or resid 189 through 204 or (resid 205 and \ (name N or name CA or name C or name O or name CB )) or resid 206 through 235 or \ (resid 236 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 7 through 286 or (resid 287 through 288 and (name N or name CA or name C or name \ O or name CB )) or resid 289 through 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 345 or (resid 346 through \ 352 and (name N or name CA or name C or name O or name CB )) or resid 353 or (re \ sid 354 and (name N or name CA or name C or name O or name CB )) or resid 355 or \ (resid 356 through 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 through 368 or (resid 369 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 th \ rough 392 or (resid 393 through 394 and (name N or name CA or name C or name O o \ r name CB )) or resid 395 through 397 or (resid 398 through 403 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 404 through 411 and (name N o \ r name CA or name C or name O or name CB )) or resid 412 through 413 or (resid 4 \ 14 through 415 and (name N or name CA or name C or name O or name CB )) or (resi \ d 416 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 428 or (resid 429 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 445 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 446 through 462 and \ (name N or name CA or name C or name O or name CB )) or resid 463 or (resid 464 \ through 475 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 76 through 489 or (resid 490 and (name N or name CA or name C or name O or name \ CB )) or resid 491 through 493 or (resid 494 through 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 or (resid 497 through 498 and (na \ me N or name CA or name C or name O or name CB )) or resid 499 through 505 or (r \ esid 506 and (name N or name CA or name C or name O or name CB )) or resid 507 o \ r (resid 508 through 520 and (name N or name CA or name C or name O or name CB ) \ ) or resid 521 through 531 or (resid 532 and (name N or name CA or name C or nam \ e O or name CB )) or resid 533 through 546 or (resid 547 and (name N or name CA \ or name C or name O or name CB )) or resid 548 through 557 or (resid 558 and (na \ me N or name CA or name C or name O or name CB )) or resid 559 through 570 or (r \ esid 571 through 572 and (name N or name CA or name C or name O or name CB )) or \ resid 573 through 582 or (resid 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 644 or (resid \ 645 and (name N or name CA or name C or name O or name CB )) or resid 646 throu \ gh 657 or (resid 658 and (name N or name CA or name C or name O or name CB )) or \ resid 659 through 675 or (resid 676 and (name N or name CA or name C or name O \ or name CB )) or (resid 690 and (name N or name CA or name C or name O or name C \ B )) or resid 691 through 736 or (resid 737 and (name N or name CA or name C or \ name O or name CB )) or resid 738 or (resid 739 and (name N or name CA or name C \ or name O or name CB )) or resid 740 through 746 or (resid 747 through 748 and \ (name N or name CA or name C or name O or name CB )) or resid 749 through 779 or \ (resid 780 and (name N or name CA or name C or name O or name CB )) or resid 78 \ 1 through 795 or (resid 796 and (name N or name CA or name C or name O or name C \ B )) or resid 797 through 809 or (resid 810 through 813 and (name N or name CA o \ r name C or name O or name CB )) or resid 814 through 827 or (resid 856 and (nam \ e N or name CA or name C or name O or name CB )) or resid 857 through 866 or (re \ sid 867 through 868 and (name N or name CA or name C or name O or name CB )) or \ resid 869 through 920 or (resid 921 and (name N or name CA or name C or name O o \ r name CB )) or resid 922 through 941 or resid 943 through 949 or (resid 950 and \ (name N or name CA or name C or name O or name CB )) or resid 951 through 972 o \ r (resid 973 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 74 through 981 or (resid 982 and (name N or name CA or name C or name O or name \ CB )) or resid 983 through 984 or (resid 985 and (name N or name CA or name C or \ name O or name CB )) or resid 986 through 1044 or (resid 1045 and (name N or na \ me CA or name C or name O or name CB )) or resid 1046 through 1054 or (resid 105 \ 5 through 1056 and (name N or name CA or name C or name O or name CB )) or resid \ 1057 through 1099 or (resid 1100 and (name N or name CA or name C or name O or \ name CB )) or resid 1101 through 1122 or (resid 1123 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1124 or (resid 1125 and (name N or name C \ A or name C or name O or name CB )) or resid 1126 through 1143 or (resid 1144 th \ rough 1145 and (name N or name CA or name C or name O or name CB )) or resid 130 \ 1 through 1310)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 65 or (resid 66 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 98 or (resid 99 throu \ gh 100 and (name N or name CA or name C or name O or name CB )) or resid 101 or \ (resid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 \ through 107 or (resid 108 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or resid 116 through 131 or (resid 132 through 135 \ and (name N or name CA or name C or name O or name CB )) or resid 139 or (resid \ 140 and (name N or name CA or name C or name O or name CB )) or resid 166 throug \ h 172 or (resid 188 and (name N or name CA or name C or name O or name CB )) or \ resid 189 through 196 or resid 200 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 238 or (resid 239 thr \ ough 240 and (name N or name CA or name C or name O or name CB )) or resid 241 t \ hrough 304 or (resid 305 and (name N or name CA or name C or name O or name CB ) \ ) or resid 306 through 315 or (resid 316 through 317 and (name N or name CA or n \ ame C or name O or name CB )) or resid 318 through 331 or (resid 332 through 334 \ and (name N or name CA or name C or name O or name CB )) or resid 335 through 3 \ 39 or (resid 340 through 341 and (name N or name CA or name C or name O or name \ CB )) or resid 342 through 350 or (resid 351 through 352 and (name N or name CA \ or name C or name O or name CB )) or resid 353 through 361 or (resid 362 through \ 363 and (name N or name CA or name C or name O or name CB )) or resid 364 throu \ gh 366 or (resid 367 through 378 and (name N or name CA or name C or name O or n \ ame CB )) or resid 379 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 567 or (resid 568 thr \ ough 572 and (name N or name CA or name C or name O or name CB )) or resid 573 t \ hrough 582 or (resid 583 and (name N or name CA or name C or name O or name CB ) \ ) or resid 584 through 657 or (resid 658 and (name N or name CA or name C or nam \ e O or name CB )) or resid 659 through 674 or (resid 675 through 690 and (name N \ or name CA or name C or name O or name CB )) or resid 691 through 720 or (resid \ 721 and (name N or name CA or name C or name O or name CB )) or resid 722 throu \ gh 779 or (resid 780 and (name N or name CA or name C or name O or name CB )) or \ resid 781 through 858 or (resid 859 and (name N or name CA or name C or name O \ or name CB )) or resid 860 through 867 or (resid 868 and (name N or name CA or n \ ame C or name O or name CB )) or resid 869 through 940 or (resid 941 and (name N \ or name CA or name C or name O or name CB )) or resid 943 through 989 or (resid \ 990 and (name N or name CA or name C or name O or name CB )) or resid 991 throu \ gh 1016 or (resid 1017 and (name N or name CA or name C or name O or name CB )) \ or resid 1018 through 1044 or (resid 1045 and (name N or name CA or name C or na \ me O or name CB )) or resid 1046 through 1117 or (resid 1118 and (name N or name \ CA or name C or name O or name CB )) or resid 1119 through 1122 or (resid 1123 \ and (name N or name CA or name C or name O or name CB )) or resid 1124 or (resid \ 1125 and (name N or name CA or name C or name O or name CB )) or resid 1126 thr \ ough 1143 or (resid 1144 through 1145 and (name N or name CA or name C or name O \ or name CB )) or resid 1302 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 55.800 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.015 0.316 23873 Z= 0.794 Angle : 1.437 21.985 32757 Z= 0.950 Chirality : 0.096 0.740 4008 Planarity : 0.005 0.030 4166 Dihedral : 10.155 89.166 8862 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.16 % Favored : 97.75 % Rotamer: Outliers : 0.19 % Allowed : 0.76 % Favored : 99.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3060 helix: 0.19 (0.16), residues: 844 sheet: 0.99 (0.19), residues: 685 loop : 0.18 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP B1102 HIS 0.006 0.002 HIS C1083 PHE 0.028 0.004 PHE B 898 TYR 0.043 0.005 TYR C 351 ARG 0.004 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.06588 ( 46) link_NAG-ASN : angle 2.71656 ( 138) link_BETA1-4 : bond 0.06494 ( 13) link_BETA1-4 : angle 3.59543 ( 39) hydrogen bonds : bond 0.15658 ( 1155) hydrogen bonds : angle 7.72545 ( 3192) SS BOND : bond 0.06909 ( 39) SS BOND : angle 4.12031 ( 78) covalent geometry : bond 0.01403 (23775) covalent geometry : angle 1.41157 (32502) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 453 time to evaluate : 2.807 Fit side-chains REVERT: A 127 VAL cc_start: 0.8463 (t) cc_final: 0.8213 (m) REVERT: A 403 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7263 (mtm110) REVERT: B 396 TYR cc_start: 0.6995 (m-80) cc_final: 0.6747 (m-80) REVERT: B 508 TYR cc_start: 0.6715 (m-80) cc_final: 0.6441 (m-80) outliers start: 4 outliers final: 0 residues processed: 456 average time/residue: 0.3619 time to fit residues: 254.4395 Evaluate side-chains 201 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 130 optimal weight: 0.0870 chunk 80 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 50.0000 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 0.1980 chunk 180 optimal weight: 0.5980 chunk 281 optimal weight: 0.4980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 564 GLN A 580 GLN B 540 ASN B 762 GLN B1048 HIS B1071 GLN B1135 ASN C 49 HIS C 321 GLN C 935 GLN C 954 GLN C 965 GLN C1002 GLN C1071 GLN C1119 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.163437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131759 restraints weight = 34571.967| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.38 r_work: 0.3345 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23873 Z= 0.145 Angle : 0.638 15.821 32757 Z= 0.325 Chirality : 0.048 0.964 4008 Planarity : 0.004 0.036 4166 Dihedral : 5.320 46.398 4527 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.14 % Favored : 98.79 % Rotamer: Outliers : 1.89 % Allowed : 7.28 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.14), residues: 3060 helix: 2.11 (0.18), residues: 820 sheet: 0.89 (0.18), residues: 699 loop : 0.11 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.005 0.001 HIS C 49 PHE 0.025 0.002 PHE B 400 TYR 0.023 0.002 TYR C1067 ARG 0.005 0.001 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 46) link_NAG-ASN : angle 3.18753 ( 138) link_BETA1-4 : bond 0.00652 ( 13) link_BETA1-4 : angle 2.05649 ( 39) hydrogen bonds : bond 0.04750 ( 1155) hydrogen bonds : angle 5.84910 ( 3192) SS BOND : bond 0.00493 ( 39) SS BOND : angle 1.65746 ( 78) covalent geometry : bond 0.00316 (23775) covalent geometry : angle 0.59596 (32502) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 2.531 Fit side-chains REVERT: A 105 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8092 (pt) REVERT: A 237 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8015 (mtm-85) REVERT: A 356 LYS cc_start: 0.7385 (tttt) cc_final: 0.7181 (ttpt) REVERT: A 365 TYR cc_start: 0.8469 (m-80) cc_final: 0.7340 (m-80) REVERT: A 403 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7274 (mtm110) REVERT: A 823 PHE cc_start: 0.7940 (t80) cc_final: 0.7681 (t80) REVERT: A 875 SER cc_start: 0.9047 (t) cc_final: 0.8611 (m) REVERT: A 900 MET cc_start: 0.8742 (ttm) cc_final: 0.8321 (mtp) REVERT: A 949 GLN cc_start: 0.8535 (tp40) cc_final: 0.8299 (tp-100) REVERT: B 396 TYR cc_start: 0.6922 (m-80) cc_final: 0.6483 (m-80) REVERT: B 421 TYR cc_start: 0.8004 (m-10) cc_final: 0.7773 (m-10) REVERT: B 1071 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6855 (mt0) outliers start: 40 outliers final: 19 residues processed: 272 average time/residue: 0.3160 time to fit residues: 142.1003 Evaluate side-chains 201 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 198 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 266 optimal weight: 0.0770 chunk 166 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1048 HIS B 655 HIS B1071 GLN C 321 GLN C1048 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.160923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129249 restraints weight = 34407.950| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.34 r_work: 0.3284 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 23873 Z= 0.160 Angle : 0.584 13.456 32757 Z= 0.294 Chirality : 0.046 0.663 4008 Planarity : 0.004 0.037 4166 Dihedral : 4.849 59.871 4527 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.57 % Favored : 98.40 % Rotamer: Outliers : 2.17 % Allowed : 8.27 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 3060 helix: 2.32 (0.18), residues: 822 sheet: 0.66 (0.18), residues: 726 loop : 0.06 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.009 0.001 HIS B 655 PHE 0.021 0.002 PHE B 400 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 46) link_NAG-ASN : angle 2.92840 ( 138) link_BETA1-4 : bond 0.00664 ( 13) link_BETA1-4 : angle 1.84067 ( 39) hydrogen bonds : bond 0.04168 ( 1155) hydrogen bonds : angle 5.46970 ( 3192) SS BOND : bond 0.00540 ( 39) SS BOND : angle 1.33498 ( 78) covalent geometry : bond 0.00368 (23775) covalent geometry : angle 0.54671 (32502) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 2.499 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8099 (pt) REVERT: A 237 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8172 (mtm-85) REVERT: A 365 TYR cc_start: 0.8530 (m-80) cc_final: 0.8261 (m-80) REVERT: A 823 PHE cc_start: 0.8064 (t80) cc_final: 0.7813 (t80) REVERT: A 875 SER cc_start: 0.9104 (t) cc_final: 0.8609 (m) REVERT: A 1111 GLU cc_start: 0.8325 (tt0) cc_final: 0.8071 (tt0) REVERT: A 1119 ASN cc_start: 0.7527 (m-40) cc_final: 0.7264 (m110) REVERT: B 28 TYR cc_start: 0.7777 (m-10) cc_final: 0.7576 (m-10) REVERT: B 396 TYR cc_start: 0.7201 (m-80) cc_final: 0.6763 (m-80) REVERT: B 421 TYR cc_start: 0.7973 (m-10) cc_final: 0.7669 (m-10) REVERT: B 661 GLU cc_start: 0.7947 (tp30) cc_final: 0.7691 (tp30) outliers start: 46 outliers final: 29 residues processed: 242 average time/residue: 0.3083 time to fit residues: 123.3625 Evaluate side-chains 203 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 129 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 162 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN C 207 HIS C 321 GLN C1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.151959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123094 restraints weight = 34981.740| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.69 r_work: 0.3244 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23873 Z= 0.181 Angle : 0.592 18.973 32757 Z= 0.296 Chirality : 0.049 1.007 4008 Planarity : 0.004 0.037 4166 Dihedral : 4.910 54.233 4527 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.27 % Favored : 98.66 % Rotamer: Outliers : 2.55 % Allowed : 9.13 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3060 helix: 2.43 (0.18), residues: 814 sheet: 0.40 (0.18), residues: 725 loop : -0.03 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 353 HIS 0.004 0.001 HIS C1083 PHE 0.018 0.002 PHE B 643 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 46) link_NAG-ASN : angle 3.27615 ( 138) link_BETA1-4 : bond 0.00535 ( 13) link_BETA1-4 : angle 1.60491 ( 39) hydrogen bonds : bond 0.04018 ( 1155) hydrogen bonds : angle 5.34105 ( 3192) SS BOND : bond 0.00530 ( 39) SS BOND : angle 1.51860 ( 78) covalent geometry : bond 0.00423 (23775) covalent geometry : angle 0.54680 (32502) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 3.657 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8261 (mtpp) REVERT: A 105 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8191 (pt) REVERT: A 237 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8186 (mtm-85) REVERT: A 354 ASN cc_start: 0.7696 (t0) cc_final: 0.7261 (p0) REVERT: A 365 TYR cc_start: 0.8363 (m-80) cc_final: 0.8093 (m-80) REVERT: A 396 TYR cc_start: 0.7523 (m-80) cc_final: 0.7104 (m-80) REVERT: A 823 PHE cc_start: 0.8134 (t80) cc_final: 0.7886 (t80) REVERT: A 875 SER cc_start: 0.9082 (t) cc_final: 0.8599 (m) REVERT: A 934 ILE cc_start: 0.9016 (mm) cc_final: 0.8675 (mm) REVERT: A 1111 GLU cc_start: 0.8202 (tt0) cc_final: 0.7950 (tt0) REVERT: B 661 GLU cc_start: 0.8010 (tp30) cc_final: 0.7808 (tp30) outliers start: 54 outliers final: 40 residues processed: 232 average time/residue: 0.3217 time to fit residues: 124.2561 Evaluate side-chains 210 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 182 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 chunk 283 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 317 ASN B 87 ASN B 115 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116738 restraints weight = 34563.641| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.16 r_work: 0.3300 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23873 Z= 0.179 Angle : 0.576 11.964 32757 Z= 0.289 Chirality : 0.048 0.664 4008 Planarity : 0.004 0.037 4166 Dihedral : 4.860 55.323 4527 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.33 % Rotamer: Outliers : 2.79 % Allowed : 9.60 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.15), residues: 3060 helix: 2.41 (0.18), residues: 820 sheet: 0.29 (0.18), residues: 708 loop : -0.09 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.004 0.001 HIS C1083 PHE 0.018 0.002 PHE B 643 TYR 0.020 0.001 TYR B 269 ARG 0.004 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 46) link_NAG-ASN : angle 2.85961 ( 138) link_BETA1-4 : bond 0.00502 ( 13) link_BETA1-4 : angle 1.44125 ( 39) hydrogen bonds : bond 0.03857 ( 1155) hydrogen bonds : angle 5.25911 ( 3192) SS BOND : bond 0.00504 ( 39) SS BOND : angle 1.42502 ( 78) covalent geometry : bond 0.00423 (23775) covalent geometry : angle 0.54027 (32502) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 2.484 Fit side-chains REVERT: A 41 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: A 105 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8098 (pt) REVERT: A 237 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8334 (mtm-85) REVERT: A 354 ASN cc_start: 0.7872 (t0) cc_final: 0.7198 (p0) REVERT: A 365 TYR cc_start: 0.8629 (m-80) cc_final: 0.8216 (m-80) REVERT: A 875 SER cc_start: 0.9162 (t) cc_final: 0.8656 (m) REVERT: A 934 ILE cc_start: 0.9041 (mm) cc_final: 0.8674 (mm) REVERT: A 1111 GLU cc_start: 0.8555 (tt0) cc_final: 0.8294 (tt0) REVERT: B 41 LYS cc_start: 0.8113 (mttt) cc_final: 0.7832 (mtpt) REVERT: C 203 ILE cc_start: 0.8853 (mt) cc_final: 0.8502 (tt) outliers start: 59 outliers final: 43 residues processed: 225 average time/residue: 0.3189 time to fit residues: 119.8333 Evaluate side-chains 208 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 57 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 80 optimal weight: 0.0070 chunk 85 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116256 restraints weight = 34324.685| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.42 r_work: 0.3291 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23873 Z= 0.136 Angle : 0.553 13.578 32757 Z= 0.277 Chirality : 0.046 0.599 4008 Planarity : 0.004 0.036 4166 Dihedral : 4.626 51.851 4527 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.65 % Allowed : 9.98 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.15), residues: 3060 helix: 2.49 (0.18), residues: 828 sheet: 0.28 (0.18), residues: 710 loop : -0.07 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.003 0.001 HIS B1048 PHE 0.018 0.001 PHE B 392 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 46) link_NAG-ASN : angle 2.83161 ( 138) link_BETA1-4 : bond 0.00486 ( 13) link_BETA1-4 : angle 1.35261 ( 39) hydrogen bonds : bond 0.03646 ( 1155) hydrogen bonds : angle 5.13965 ( 3192) SS BOND : bond 0.00470 ( 39) SS BOND : angle 1.74132 ( 78) covalent geometry : bond 0.00316 (23775) covalent geometry : angle 0.51413 (32502) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 2.501 Fit side-chains REVERT: A 41 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8474 (mtpp) REVERT: A 105 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8058 (pt) REVERT: A 237 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8362 (mtm-85) REVERT: A 354 ASN cc_start: 0.7895 (t0) cc_final: 0.7168 (p0) REVERT: A 365 TYR cc_start: 0.8659 (m-80) cc_final: 0.8231 (m-80) REVERT: A 369 TYR cc_start: 0.8009 (t80) cc_final: 0.7809 (t80) REVERT: A 875 SER cc_start: 0.9182 (t) cc_final: 0.8679 (m) REVERT: A 934 ILE cc_start: 0.9016 (mm) cc_final: 0.8657 (mm) REVERT: B 41 LYS cc_start: 0.8123 (mttt) cc_final: 0.7817 (mtpt) REVERT: B 858 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8193 (mt) REVERT: C 983 ARG cc_start: 0.7468 (ttm170) cc_final: 0.7254 (ttm170) outliers start: 56 outliers final: 42 residues processed: 213 average time/residue: 0.2924 time to fit residues: 104.9336 Evaluate side-chains 209 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 90 optimal weight: 1.9990 chunk 269 optimal weight: 0.5980 chunk 139 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B1088 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.155971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115107 restraints weight = 34672.205| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.14 r_work: 0.3265 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 23873 Z= 0.249 Angle : 0.640 16.399 32757 Z= 0.317 Chirality : 0.049 0.579 4008 Planarity : 0.004 0.040 4166 Dihedral : 4.972 58.618 4527 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.88 % Allowed : 10.17 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.15), residues: 3060 helix: 2.34 (0.18), residues: 825 sheet: 0.24 (0.19), residues: 694 loop : -0.32 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 353 HIS 0.005 0.001 HIS B1048 PHE 0.018 0.002 PHE B 392 TYR 0.020 0.002 TYR C1067 ARG 0.006 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 46) link_NAG-ASN : angle 3.08308 ( 138) link_BETA1-4 : bond 0.00361 ( 13) link_BETA1-4 : angle 1.40110 ( 39) hydrogen bonds : bond 0.04126 ( 1155) hydrogen bonds : angle 5.30758 ( 3192) SS BOND : bond 0.00770 ( 39) SS BOND : angle 1.81664 ( 78) covalent geometry : bond 0.00600 (23775) covalent geometry : angle 0.60219 (32502) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 2.819 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8525 (mtpp) REVERT: A 105 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8101 (pt) REVERT: A 237 ARG cc_start: 0.8620 (mtm-85) cc_final: 0.8327 (mtm-85) REVERT: A 354 ASN cc_start: 0.7922 (t0) cc_final: 0.7261 (p0) REVERT: A 369 TYR cc_start: 0.8195 (t80) cc_final: 0.7987 (t80) REVERT: A 934 ILE cc_start: 0.9087 (mm) cc_final: 0.8736 (mm) REVERT: B 41 LYS cc_start: 0.8065 (mttt) cc_final: 0.7771 (mtpt) REVERT: B 858 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8207 (mt) REVERT: C 203 ILE cc_start: 0.8826 (mt) cc_final: 0.8503 (tt) outliers start: 61 outliers final: 49 residues processed: 208 average time/residue: 0.3075 time to fit residues: 107.6616 Evaluate side-chains 201 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 116 optimal weight: 0.0170 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 279 optimal weight: 0.5980 chunk 285 optimal weight: 0.4980 chunk 120 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 305 optimal weight: 9.9990 chunk 180 optimal weight: 0.0050 chunk 37 optimal weight: 0.8980 overall best weight: 0.3432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1071 GLN C 321 GLN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116227 restraints weight = 34546.905| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.25 r_work: 0.3321 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 23873 Z= 0.109 Angle : 0.539 15.205 32757 Z= 0.269 Chirality : 0.045 0.502 4008 Planarity : 0.003 0.035 4166 Dihedral : 4.494 53.435 4527 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.22 % Allowed : 11.25 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.15), residues: 3060 helix: 2.58 (0.18), residues: 833 sheet: 0.22 (0.19), residues: 691 loop : -0.15 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 353 HIS 0.002 0.001 HIS A 207 PHE 0.019 0.001 PHE B 392 TYR 0.019 0.001 TYR B 495 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 46) link_NAG-ASN : angle 2.72554 ( 138) link_BETA1-4 : bond 0.00475 ( 13) link_BETA1-4 : angle 1.21647 ( 39) hydrogen bonds : bond 0.03433 ( 1155) hydrogen bonds : angle 5.06840 ( 3192) SS BOND : bond 0.00609 ( 39) SS BOND : angle 1.63718 ( 78) covalent geometry : bond 0.00245 (23775) covalent geometry : angle 0.50327 (32502) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8378 (mtpp) REVERT: A 105 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8014 (pt) REVERT: A 237 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8411 (mtm-85) REVERT: A 354 ASN cc_start: 0.7894 (t0) cc_final: 0.7144 (p0) REVERT: A 505 TYR cc_start: 0.8384 (m-80) cc_final: 0.8108 (m-10) REVERT: A 900 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8404 (mtp) REVERT: A 934 ILE cc_start: 0.9031 (mm) cc_final: 0.8662 (mm) REVERT: B 41 LYS cc_start: 0.8105 (mttt) cc_final: 0.7860 (mtpt) outliers start: 47 outliers final: 35 residues processed: 207 average time/residue: 0.3143 time to fit residues: 108.5264 Evaluate side-chains 193 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 294 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 285 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B1002 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.158040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117498 restraints weight = 34540.069| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.33 r_work: 0.3312 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23873 Z= 0.155 Angle : 0.564 14.822 32757 Z= 0.281 Chirality : 0.046 0.479 4008 Planarity : 0.004 0.080 4166 Dihedral : 4.421 44.063 4527 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.08 % Allowed : 11.58 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.15), residues: 3060 helix: 2.56 (0.18), residues: 833 sheet: 0.25 (0.19), residues: 690 loop : -0.16 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.004 0.001 HIS B1048 PHE 0.021 0.001 PHE B 392 TYR 0.039 0.001 TYR B 495 ARG 0.007 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 46) link_NAG-ASN : angle 2.68049 ( 138) link_BETA1-4 : bond 0.00417 ( 13) link_BETA1-4 : angle 1.22349 ( 39) hydrogen bonds : bond 0.03589 ( 1155) hydrogen bonds : angle 5.08643 ( 3192) SS BOND : bond 0.00638 ( 39) SS BOND : angle 1.81921 ( 78) covalent geometry : bond 0.00367 (23775) covalent geometry : angle 0.52999 (32502) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8396 (mtpp) REVERT: A 105 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8028 (pt) REVERT: A 237 ARG cc_start: 0.8636 (mtm-85) cc_final: 0.8396 (mtm-85) REVERT: A 354 ASN cc_start: 0.7865 (t0) cc_final: 0.7131 (p0) REVERT: A 505 TYR cc_start: 0.8418 (m-80) cc_final: 0.8133 (m-10) REVERT: A 646 ARG cc_start: 0.8653 (tpt170) cc_final: 0.8337 (mmt90) REVERT: A 875 SER cc_start: 0.9121 (t) cc_final: 0.8610 (m) REVERT: A 934 ILE cc_start: 0.9020 (mm) cc_final: 0.8664 (mm) REVERT: B 41 LYS cc_start: 0.8163 (mttt) cc_final: 0.7834 (mtpt) REVERT: B 421 TYR cc_start: 0.7848 (m-10) cc_final: 0.7522 (m-10) outliers start: 44 outliers final: 36 residues processed: 198 average time/residue: 0.3067 time to fit residues: 101.5150 Evaluate side-chains 196 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 218 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 241 optimal weight: 50.0000 chunk 122 optimal weight: 2.9990 chunk 245 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.157707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117571 restraints weight = 34482.762| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.16 r_work: 0.3299 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23873 Z= 0.166 Angle : 0.565 14.674 32757 Z= 0.282 Chirality : 0.046 0.466 4008 Planarity : 0.004 0.072 4166 Dihedral : 4.392 37.877 4527 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.84 % Allowed : 11.87 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.15), residues: 3060 helix: 2.52 (0.18), residues: 837 sheet: 0.25 (0.19), residues: 678 loop : -0.16 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 353 HIS 0.004 0.001 HIS B1048 PHE 0.018 0.001 PHE B 392 TYR 0.020 0.001 TYR B 495 ARG 0.008 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 46) link_NAG-ASN : angle 2.67460 ( 138) link_BETA1-4 : bond 0.00422 ( 13) link_BETA1-4 : angle 1.19546 ( 39) hydrogen bonds : bond 0.03654 ( 1155) hydrogen bonds : angle 5.09162 ( 3192) SS BOND : bond 0.00638 ( 39) SS BOND : angle 1.52787 ( 78) covalent geometry : bond 0.00395 (23775) covalent geometry : angle 0.53346 (32502) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8381 (mtpp) REVERT: A 105 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8064 (pt) REVERT: A 237 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8419 (mtm-85) REVERT: A 354 ASN cc_start: 0.7959 (t0) cc_final: 0.7216 (p0) REVERT: A 505 TYR cc_start: 0.8392 (m-80) cc_final: 0.8101 (m-10) REVERT: A 646 ARG cc_start: 0.8640 (tpt170) cc_final: 0.8324 (mmt90) REVERT: A 934 ILE cc_start: 0.9064 (mm) cc_final: 0.8708 (mm) REVERT: B 41 LYS cc_start: 0.8152 (mttt) cc_final: 0.7871 (mtpt) REVERT: B 421 TYR cc_start: 0.7906 (m-10) cc_final: 0.7660 (m-10) outliers start: 39 outliers final: 34 residues processed: 192 average time/residue: 0.3119 time to fit residues: 100.6324 Evaluate side-chains 193 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 214 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 118 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 236 optimal weight: 50.0000 chunk 306 optimal weight: 40.0000 chunk 283 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 301 optimal weight: 0.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B1002 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.157461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114959 restraints weight = 34598.576| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.32 r_work: 0.3279 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23873 Z= 0.180 Angle : 0.575 14.527 32757 Z= 0.287 Chirality : 0.047 0.456 4008 Planarity : 0.004 0.067 4166 Dihedral : 4.422 32.763 4527 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.10 % Rotamer: Outliers : 2.27 % Allowed : 11.49 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.15), residues: 3060 helix: 2.50 (0.18), residues: 834 sheet: 0.23 (0.19), residues: 684 loop : -0.16 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 353 HIS 0.005 0.001 HIS B1048 PHE 0.019 0.001 PHE B 392 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 46) link_NAG-ASN : angle 2.65940 ( 138) link_BETA1-4 : bond 0.00415 ( 13) link_BETA1-4 : angle 1.18818 ( 39) hydrogen bonds : bond 0.03687 ( 1155) hydrogen bonds : angle 5.11035 ( 3192) SS BOND : bond 0.00610 ( 39) SS BOND : angle 1.62569 ( 78) covalent geometry : bond 0.00431 (23775) covalent geometry : angle 0.54312 (32502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14428.41 seconds wall clock time: 248 minutes 36.49 seconds (14916.49 seconds total)