Starting phenix.real_space_refine on Fri Jun 20 07:50:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpc_26051/06_2025/7tpc_26051.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpc_26051/06_2025/7tpc_26051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tpc_26051/06_2025/7tpc_26051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpc_26051/06_2025/7tpc_26051.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpc_26051/06_2025/7tpc_26051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpc_26051/06_2025/7tpc_26051.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.131 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 100 5.16 5 C 14770 2.51 5 N 3834 2.21 5 O 4495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 23199 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7700 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 48, 'TRANS': 956} Chain breaks: 10 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 7070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7070 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 46, 'TRANS': 928} Chain breaks: 10 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7617 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 48, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 12, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 140 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: "E" 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: "F" 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: "G" 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: "A" 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: "B" 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 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: 14.12, per 1000 atoms: 0.61 Number of scatterers: 23199 At special positions: 0 Unit cell: (130.68, 135, 172.8, 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 100 16.00 O 4495 8.00 N 3834 7.00 C 14770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 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=2.01 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 717 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 2.8 seconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5594 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 44 sheets defined 27.2% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 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 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.756A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.633A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.977A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.656A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.690A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.764A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.445A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.972A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.567A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.798A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.765A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.902A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.994A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.523A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (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: 3.506A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.373A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.970A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.176A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.802A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.067A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.940A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (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 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.828A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.388A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.852A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.761A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 6.044A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.991A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.830A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 4.089A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.518A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.594A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.883A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.427A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.320A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.946A 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 removed outlier: 4.374A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 454 removed outlier: 4.076A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) 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: 6.091A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 7.010A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 719 removed outlier: 6.229A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 722 through 728 removed outlier: 4.484A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.955A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 9.056A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.844A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.755A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.318A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.460A pdb=" N ILE B 584 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 378 through 379 removed outlier: 3.601A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.968A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AC8, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.693A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.436A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.436A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.987A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.654A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.476A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.028A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.846A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.884A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.616A 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 728 removed outlier: 6.154A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.355A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 5.037A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) 987 hydrogen bonds defined for protein. 2691 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: 10.56 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6052 1.33 - 1.46: 4694 1.46 - 1.58: 12812 1.58 - 1.70: 0 1.70 - 1.83: 124 Bond restraints: 23682 Sorted by residual: bond pdb=" CA PRO B 792 " pdb=" C PRO B 792 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.26e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.514 1.539 -0.024 5.50e-03 3.31e+04 1.97e+01 bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.487 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C5 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.46e+01 ... (remaining 23677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 31846 4.72 - 9.44: 446 9.44 - 14.16: 4 14.16 - 18.88: 0 18.88 - 23.60: 1 Bond angle restraints: 32297 Sorted by residual: angle pdb=" CA PHE C 592 " pdb=" CB PHE C 592 " pdb=" CG PHE C 592 " ideal model delta sigma weight residual 113.80 122.40 -8.60 1.00e+00 1.00e+00 7.39e+01 angle pdb=" CB LEU B 212 " pdb=" CG LEU B 212 " pdb=" CD1 LEU B 212 " ideal model delta sigma weight residual 110.70 134.30 -23.60 3.00e+00 1.11e-01 6.19e+01 angle pdb=" C VAL A 620 " pdb=" N PRO A 621 " pdb=" CA PRO A 621 " ideal model delta sigma weight residual 119.84 127.39 -7.55 1.25e+00 6.40e-01 3.65e+01 angle pdb=" CA PHE C 643 " pdb=" CB PHE C 643 " pdb=" CG PHE C 643 " ideal model delta sigma weight residual 113.80 119.77 -5.97 1.00e+00 1.00e+00 3.56e+01 angle pdb=" CA PHE B 643 " pdb=" CB PHE B 643 " pdb=" CG PHE B 643 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.52e+01 ... (remaining 32292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13552 17.78 - 35.57: 1013 35.57 - 53.35: 153 53.35 - 71.14: 43 71.14 - 88.92: 32 Dihedral angle restraints: 14793 sinusoidal: 6133 harmonic: 8660 Sorted by residual: dihedral pdb=" C TYR B 200 " pdb=" N TYR B 200 " pdb=" CA TYR B 200 " pdb=" CB TYR B 200 " ideal model delta harmonic sigma weight residual -122.60 -140.67 18.07 0 2.50e+00 1.60e-01 5.23e+01 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 -146.78 60.78 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" N TYR B 200 " pdb=" C TYR B 200 " pdb=" CA TYR B 200 " pdb=" CB TYR B 200 " ideal model delta harmonic sigma weight residual 122.80 138.16 -15.36 0 2.50e+00 1.60e-01 3.77e+01 ... (remaining 14790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 3921 0.267 - 0.534: 19 0.534 - 0.801: 2 0.801 - 1.068: 0 1.068 - 1.335: 1 Chirality restraints: 3943 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.76e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.60e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.37e+01 ... (remaining 3940 not shown) Planarity restraints: 4141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.207 2.00e-02 2.50e+03 1.14e-01 3.27e+02 pdb=" CG TRP A 886 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.125 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.077 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " -0.167 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.122 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.144 2.00e-02 2.50e+03 1.54e-01 2.96e+02 pdb=" CG ASN A1134 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.237 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.136 2.00e-02 2.50e+03 1.49e-01 2.77e+02 pdb=" CG ASN B 709 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.236 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " -0.180 2.00e-02 2.50e+03 ... (remaining 4138 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 12188 2.99 - 3.47: 24751 3.47 - 3.94: 39595 3.94 - 4.42: 44859 4.42 - 4.90: 71920 Nonbonded interactions: 193313 Sorted by model distance: nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.509 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.515 3.040 nonbonded pdb=" O LYS A 964 " pdb=" OG SER A 967 " model vdw 2.526 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.527 3.040 ... (remaining 193308 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 197 or (resid 198 and (name N or name CA or name C o \ r name O or name CB )) or resid 199 through 210 or (resid 211 and (name N or nam \ e CA or name C or name O or name CB )) or resid 212 or (resid 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 or (resid 215 and (name \ N or name CA or name C or name O or name CB )) or resid 216 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 238 or (resid 239 and (name N or name CA or name C or name O \ or name CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 a \ nd (name N or name CA or name C or name O or name CB )) or resid 310 through 323 \ or (resid 324 and (name N or name CA or name C or name O or name CB )) or resid \ 325 through 332 or (resid 333 through 334 and (name N or name CA or name C or n \ ame O or name CB )) or resid 335 through 345 or (resid 346 through 360 and (name \ N or name CA or name C or name O or name CB )) or resid 361 or (resid 362 throu \ gh 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 (resid 385 through 390 and (name N or name CA or name C or n \ ame O or name CB )) or resid 391 or (resid 392 through 403 and (name N or name C \ A or name C or name O or name CB )) or (resid 404 through 411 and (name N or nam \ e CA or name C or name O or name CB )) or resid 412 through 413 or (resid 414 th \ rough 415 and (name N or name CA or name C or name O or name CB )) or resid 416 \ or (resid 417 through 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 427 or (resid 428 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 44 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 457 or (resi \ d 462 and (name N or name CA or name C or name O or name CB )) or resid 463 or ( \ resid 464 through 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 491 or (resid 492 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 (name N or name CA or \ name C or name O or name CB )) or resid 499 or (resid 500 through 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (na \ me N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 thr \ ough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 5 through 528 or (resid 529 and (name N or name CA or name C or name O or name C \ B )) or resid 530 through 553 or (resid 554 and (name N or name CA or name C or \ name O or name CB )) or resid 555 through 793 or (resid 794 and (name N or name \ CA or name C or name O or name CB )) or resid 795 or (resid 796 and (name N or n \ ame CA or name C or name O or name CB )) or resid 797 through 810 or (resid 811 \ and (name N or name CA or name C or name O or name CB )) or resid 813 through 82 \ 7 or resid 856 through 866 or (resid 867 through 868 and (name N or name CA or n \ ame C or name O or name CB )) or resid 869 through 939 or (resid 940 and (name N \ or name CA or name C or name O or name CB )) or resid 941 through 984 or (resid \ 985 and (name N or name CA or name C or name O or name CB )) or resid 986 throu \ gh 987 or (resid 988 through 989 and (name N or name CA or name C or name O or n \ ame CB )) or resid 990 through 1141 or (resid 1142 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 11 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 1147 or res \ id 1301 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 197 or (resid 198 and (name N or name CA or name C or name O or name CB ) \ ) or resid 199 through 210 or (resid 211 and (name N or name CA or name C or nam \ e O or name CB )) or resid 212 or (resid 213 and (name N or name CA or name C or \ name O or name CB )) or resid 214 through 241 or (resid 242 through 263 and (na \ me N or name CA or name C or name O or name CB )) or resid 265 through 280 or (r \ esid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 442 or resid 452 or resid 462 through 501 or resid 503 th \ rough 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) \ or resid 569 through 570 or (resid 571 and (name N or name CA or name C or name \ O or name CB )) or resid 572 through 581 or (resid 582 through 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 name C or name O or name CB )) or resid 587 throug \ h 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) or \ resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name \ CA or name C or name O or name CB )) or resid 746 through 810 or (resid 811 and \ (name N or name CA or name C or name O or name CB )) or resid 813 through 827 o \ r resid 856 through 866 or (resid 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 or name CB )) or resid 922 through 939 or (resid 94 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or re \ sid 986 through 987 or (resid 988 through 989 and (name N or name CA or name C o \ r name O or name CB )) or resid 990 through 1072 or (resid 1073 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1074 through 1117 or (resid 11 \ 18 and (name N or name CA or name C or name O or name CB )) or resid 1119 throug \ h 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O or \ name CB )) or resid 1147 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 197 through 217 or (resid 218 and (name N o \ r name CA or name C or name O or name CB )) or resid 219 through 223 or (resid 2 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) or r \ esid 240 through 308 or (resid 309 and (name N or name CA or name C or name O or \ name CB )) or resid 310 through 332 or (resid 333 through 334 and (name N or na \ me CA or name C or name O or name CB )) or resid 335 through 344 or (resid 345 t \ hrough 360 and (name N or name CA or name C or name O or name CB )) or resid 361 \ or (resid 362 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 nam \ e 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 (resid 385 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 or (resid 392 through 403 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 404 through 41 \ 1 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 (resid 416 through 425 and (name N or name CA or name C or name O or n \ ame 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 442 and \ (name N or name CA or name C or name O or name CB )) or resid 452 or resid 462 \ through 463 or (resid 464 through 466 and (name N or name CA or name C or name O \ or name CB )) or resid 491 or (resid 492 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 (name \ N or name CA or name C or name O or name CB )) or resid 499 through 500 or (resi \ d 501 and (name N or name CA or name C or name O or name CB )) or (resid 503 and \ (name N or name CA or name C or name O or name CB )) or (resid 504 through 506 \ and (name N or name CA or name C or name O or name CB )) or resid 507 or (resid \ 508 through 515 and (name N or name CA or name C or name O or name CB )) or (res \ id 522 through 524 and (name N or name CA or name C or name O or name CB )) or r \ esid 525 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 553 or (resid 554 and (name N or na \ me CA or name C or name O or name CB )) or resid 555 through 567 or (resid 568 a \ nd (name N or name CA or name C or name O or name CB )) or resid 569 through 570 \ or (resid 571 and (name N or name CA or name C or name O or name CB )) or resid \ 572 through 581 or (resid 582 through 583 and (name N or name CA or name C or n \ ame O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name C \ A or name 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 645 or \ (resid 646 through 647 and (name N or name CA or name C or name O or name CB )) \ or resid 648 through 793 or (resid 794 and (name N or name CA or name C or name \ O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C or n \ ame O or name CB )) or resid 797 through 920 or (resid 921 and (name N or name C \ A or name C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and \ (name N or name CA or name C or name O or name CB )) or resid 1074 through 1117 \ or (resid 1118 and (name N or name CA or name C or name O or name CB )) or resi \ d 1119 through 1141 or (resid 1142 and (name N or name CA or name C or name O or \ name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 56.160 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.014 0.078 23777 Z= 0.776 Angle : 1.867 23.595 32545 Z= 1.207 Chirality : 0.101 1.335 3943 Planarity : 0.016 0.218 4095 Dihedral : 13.440 88.923 9088 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 1.03 % Allowed : 8.83 % Favored : 90.14 % Rotamer: Outliers : 2.26 % Allowed : 4.85 % Favored : 92.89 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 2921 helix: -0.85 (0.17), residues: 668 sheet: -0.45 (0.26), residues: 346 loop : -1.79 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.207 0.034 TRP A 886 HIS 0.017 0.004 HIS C1048 PHE 0.126 0.015 PHE B 342 TYR 0.206 0.026 TYR B 707 ARG 0.009 0.001 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00936 ( 46) link_NAG-ASN : angle 4.80266 ( 138) link_BETA1-4 : bond 0.02326 ( 12) link_BETA1-4 : angle 5.09713 ( 36) hydrogen bonds : bond 0.15051 ( 969) hydrogen bonds : angle 8.87728 ( 2691) SS BOND : bond 0.00940 ( 37) SS BOND : angle 2.10401 ( 74) covalent geometry : bond 0.01361 (23682) covalent geometry : angle 1.83679 (32297) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 40 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8549 (ptm) cc_final: 0.8168 (ptm) REVERT: C 210 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7686 (mp) REVERT: C 632 THR cc_start: 0.6982 (m) cc_final: 0.6657 (p) REVERT: C 752 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8606 (tt) REVERT: C 873 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: C 900 MET cc_start: 0.7307 (mpt) cc_final: 0.6571 (mpp) outliers start: 53 outliers final: 14 residues processed: 93 average time/residue: 0.3651 time to fit residues: 55.9136 Evaluate side-chains 48 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 31 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 621 PRO Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 935 GLN B 52 GLN B 625 HIS B 901 GLN C 99 ASN C 762 GLN C 935 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.038670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.031790 restraints weight = 330596.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.032486 restraints weight = 206232.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.032940 restraints weight = 147931.285| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23777 Z= 0.170 Angle : 0.805 10.347 32545 Z= 0.413 Chirality : 0.048 0.299 3943 Planarity : 0.004 0.060 4095 Dihedral : 8.014 72.860 4413 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.61 % Favored : 94.11 % Rotamer: Outliers : 1.83 % Allowed : 6.26 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.31 (0.15), residues: 2921 helix: 0.58 (0.19), residues: 683 sheet: -1.00 (0.22), residues: 495 loop : -1.47 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 633 HIS 0.005 0.001 HIS B 625 PHE 0.020 0.002 PHE B 342 TYR 0.024 0.002 TYR A 204 ARG 0.005 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 46) link_NAG-ASN : angle 4.11125 ( 138) link_BETA1-4 : bond 0.00697 ( 12) link_BETA1-4 : angle 2.14519 ( 36) hydrogen bonds : bond 0.05697 ( 969) hydrogen bonds : angle 7.00290 ( 2691) SS BOND : bond 0.00338 ( 37) SS BOND : angle 1.92147 ( 74) covalent geometry : bond 0.00339 (23682) covalent geometry : angle 0.75265 (32297) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 35 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.7791 (ptm) cc_final: 0.7560 (ptm) REVERT: A 1029 MET cc_start: 0.8268 (ttm) cc_final: 0.7999 (mtt) REVERT: B 697 MET cc_start: 0.8424 (ptm) cc_final: 0.8143 (ptm) REVERT: B 738 CYS cc_start: 0.4557 (OUTLIER) cc_final: 0.4316 (p) REVERT: B 900 MET cc_start: 0.7456 (mtp) cc_final: 0.7220 (mtm) REVERT: B 1050 MET cc_start: 0.7713 (ptm) cc_final: 0.7077 (ptm) REVERT: C 210 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7291 (mp) REVERT: C 523 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8457 (p) REVERT: C 632 THR cc_start: 0.6597 (m) cc_final: 0.6289 (p) REVERT: C 873 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: C 900 MET cc_start: 0.6873 (mpt) cc_final: 0.6523 (mpp) outliers start: 43 outliers final: 22 residues processed: 77 average time/residue: 0.3670 time to fit residues: 47.5220 Evaluate side-chains 52 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 26 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 182 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 580 GLN B 914 ASN B1113 GLN ** C1048 HIS ** 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 = 0.3538 r_free = 0.3538 target = 0.037890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.031132 restraints weight = 332257.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.031791 restraints weight = 209113.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.032219 restraints weight = 150084.216| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23777 Z= 0.268 Angle : 0.797 9.837 32545 Z= 0.406 Chirality : 0.047 0.474 3943 Planarity : 0.005 0.067 4095 Dihedral : 7.619 61.651 4404 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.94 % Favored : 91.78 % Rotamer: Outliers : 2.43 % Allowed : 7.79 % Favored : 89.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.11 % 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: -1.40 (0.15), residues: 2921 helix: 0.36 (0.19), residues: 695 sheet: -0.94 (0.21), residues: 557 loop : -1.52 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 104 HIS 0.008 0.002 HIS A1048 PHE 0.025 0.002 PHE B 342 TYR 0.027 0.002 TYR A 204 ARG 0.005 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 46) link_NAG-ASN : angle 3.47927 ( 138) link_BETA1-4 : bond 0.00712 ( 12) link_BETA1-4 : angle 2.41229 ( 36) hydrogen bonds : bond 0.05688 ( 969) hydrogen bonds : angle 6.81904 ( 2691) SS BOND : bond 0.00373 ( 37) SS BOND : angle 1.56455 ( 74) covalent geometry : bond 0.00559 (23682) covalent geometry : angle 0.75890 (32297) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 27 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 873 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8461 (m-10) REVERT: B 697 MET cc_start: 0.8448 (ptm) cc_final: 0.8129 (ptm) REVERT: B 900 MET cc_start: 0.7727 (mtp) cc_final: 0.7266 (mtm) REVERT: B 906 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7217 (m-10) REVERT: B 1050 MET cc_start: 0.7974 (ptm) cc_final: 0.7409 (ptp) REVERT: C 210 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7299 (mp) REVERT: C 523 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8549 (p) REVERT: C 632 THR cc_start: 0.6516 (m) cc_final: 0.6234 (p) REVERT: C 752 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8717 (tt) REVERT: C 873 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: C 900 MET cc_start: 0.7013 (mpt) cc_final: 0.6383 (mpp) REVERT: C 1032 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7277 (m) outliers start: 57 outliers final: 26 residues processed: 83 average time/residue: 0.3475 time to fit residues: 49.6451 Evaluate side-chains 59 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 26 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 137 optimal weight: 40.0000 chunk 228 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 270 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 644 GLN C 784 GLN C 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.037772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.030941 restraints weight = 334755.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.031601 restraints weight = 210185.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.032030 restraints weight = 150903.926| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23777 Z= 0.215 Angle : 0.711 8.654 32545 Z= 0.363 Chirality : 0.045 0.451 3943 Planarity : 0.004 0.074 4095 Dihedral : 7.258 57.660 4401 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.47 % Favored : 93.32 % Rotamer: Outliers : 2.43 % Allowed : 9.45 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.33 (0.15), residues: 2921 helix: 0.62 (0.20), residues: 676 sheet: -0.81 (0.21), residues: 552 loop : -1.59 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 104 HIS 0.005 0.001 HIS C1048 PHE 0.020 0.002 PHE B 342 TYR 0.020 0.002 TYR A 204 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 46) link_NAG-ASN : angle 3.08412 ( 138) link_BETA1-4 : bond 0.00235 ( 12) link_BETA1-4 : angle 2.13028 ( 36) hydrogen bonds : bond 0.05064 ( 969) hydrogen bonds : angle 6.58281 ( 2691) SS BOND : bond 0.00300 ( 37) SS BOND : angle 1.76644 ( 74) covalent geometry : bond 0.00447 (23682) covalent geometry : angle 0.67609 (32297) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 27 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5968 (m-80) REVERT: A 873 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8448 (m-80) REVERT: B 697 MET cc_start: 0.8487 (ptm) cc_final: 0.8127 (ptm) REVERT: B 900 MET cc_start: 0.7592 (mtp) cc_final: 0.7153 (mtm) REVERT: B 1050 MET cc_start: 0.7936 (ptm) cc_final: 0.7493 (ptm) REVERT: C 328 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6040 (mmm-85) REVERT: C 523 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8564 (p) REVERT: C 546 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6218 (pp) REVERT: C 632 THR cc_start: 0.6167 (m) cc_final: 0.5927 (p) REVERT: C 740 MET cc_start: 0.8591 (tpt) cc_final: 0.8377 (tpt) REVERT: C 752 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8693 (tt) REVERT: C 873 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: C 900 MET cc_start: 0.6957 (mpt) cc_final: 0.6455 (mpp) REVERT: C 1032 CYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6802 (m) outliers start: 57 outliers final: 30 residues processed: 82 average time/residue: 0.3184 time to fit residues: 44.3858 Evaluate side-chains 64 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 26 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 137 optimal weight: 50.0000 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 675 GLN C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.037594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.030791 restraints weight = 335580.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.031432 restraints weight = 210021.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.031864 restraints weight = 151269.590| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23777 Z= 0.215 Angle : 0.697 8.900 32545 Z= 0.354 Chirality : 0.045 0.370 3943 Planarity : 0.004 0.080 4095 Dihedral : 7.126 55.649 4399 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.36 % Favored : 92.43 % Rotamer: Outliers : 2.51 % Allowed : 10.13 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.33 (0.15), residues: 2921 helix: 0.67 (0.20), residues: 667 sheet: -0.86 (0.21), residues: 551 loop : -1.58 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS C1048 PHE 0.019 0.002 PHE B 342 TYR 0.021 0.002 TYR A 204 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 46) link_NAG-ASN : angle 2.79376 ( 138) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 2.11654 ( 36) hydrogen bonds : bond 0.04970 ( 969) hydrogen bonds : angle 6.46291 ( 2691) SS BOND : bond 0.00305 ( 37) SS BOND : angle 1.92819 ( 74) covalent geometry : bond 0.00449 (23682) covalent geometry : angle 0.66520 (32297) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 25 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: A 873 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: A 1050 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8665 (ptm) REVERT: A 1126 CYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8270 (m) REVERT: B 697 MET cc_start: 0.8530 (ptm) cc_final: 0.8128 (ptm) REVERT: B 900 MET cc_start: 0.7601 (mtp) cc_final: 0.7177 (mtm) REVERT: B 1050 MET cc_start: 0.7930 (ptm) cc_final: 0.7402 (ptm) REVERT: C 63 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9142 (p) REVERT: C 210 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.6929 (mp) REVERT: C 328 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5973 (mmm-85) REVERT: C 523 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8557 (p) REVERT: C 546 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6185 (pp) REVERT: C 574 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7064 (t0) REVERT: C 740 MET cc_start: 0.8581 (tpt) cc_final: 0.8300 (tpt) REVERT: C 752 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8651 (tt) REVERT: C 873 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: C 1032 CYS cc_start: 0.7538 (OUTLIER) cc_final: 0.6759 (m) outliers start: 59 outliers final: 30 residues processed: 81 average time/residue: 0.3340 time to fit residues: 46.4284 Evaluate side-chains 68 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 25 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 8 optimal weight: 30.0000 chunk 147 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 chunk 206 optimal weight: 40.0000 chunk 194 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C1011 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 = 0.3533 r_free = 0.3533 target = 0.037630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.030826 restraints weight = 333829.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.031485 restraints weight = 208425.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.031891 restraints weight = 149676.448| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23777 Z= 0.191 Angle : 0.666 9.493 32545 Z= 0.337 Chirality : 0.045 0.426 3943 Planarity : 0.004 0.085 4095 Dihedral : 7.019 56.280 4399 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.78 % Favored : 93.05 % Rotamer: Outliers : 2.26 % Allowed : 10.69 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.30 (0.15), residues: 2921 helix: 0.76 (0.20), residues: 666 sheet: -0.86 (0.22), residues: 549 loop : -1.57 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS A1058 PHE 0.018 0.001 PHE B 342 TYR 0.018 0.002 TYR A 204 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 46) link_NAG-ASN : angle 2.75293 ( 138) link_BETA1-4 : bond 0.00264 ( 12) link_BETA1-4 : angle 2.02385 ( 36) hydrogen bonds : bond 0.04729 ( 969) hydrogen bonds : angle 6.36541 ( 2691) SS BOND : bond 0.00296 ( 37) SS BOND : angle 1.56303 ( 74) covalent geometry : bond 0.00399 (23682) covalent geometry : angle 0.63613 (32297) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 26 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5984 (m-80) REVERT: A 873 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: A 1050 MET cc_start: 0.8941 (ptt) cc_final: 0.8734 (ptm) REVERT: A 1126 CYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8187 (m) REVERT: B 697 MET cc_start: 0.8529 (ptm) cc_final: 0.8185 (ptm) REVERT: B 740 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7944 (tpt) REVERT: B 900 MET cc_start: 0.7548 (mtp) cc_final: 0.7143 (mtm) REVERT: B 1050 MET cc_start: 0.8021 (ptm) cc_final: 0.7648 (ptm) REVERT: C 63 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.9130 (p) REVERT: C 328 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.5880 (mmm-85) REVERT: C 523 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 546 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6179 (pp) REVERT: C 574 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7020 (t0) REVERT: C 740 MET cc_start: 0.8608 (tpt) cc_final: 0.8304 (tpt) REVERT: C 752 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8629 (tt) REVERT: C 873 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8559 (m-80) outliers start: 53 outliers final: 32 residues processed: 77 average time/residue: 0.3395 time to fit residues: 44.7941 Evaluate side-chains 68 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 25 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 270 optimal weight: 1.9990 chunk 5 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 chunk 31 optimal weight: 0.0270 chunk 268 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 273 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 613 GLN C 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.038147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.031304 restraints weight = 328916.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.032163 restraints weight = 209379.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.032520 restraints weight = 137450.911| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 23777 Z= 0.113 Angle : 0.592 7.503 32545 Z= 0.302 Chirality : 0.044 0.367 3943 Planarity : 0.004 0.090 4095 Dihedral : 6.299 56.570 4399 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.11 % Rotamer: Outliers : 2.00 % Allowed : 10.86 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.04 (0.15), residues: 2921 helix: 1.00 (0.20), residues: 669 sheet: -0.77 (0.22), residues: 545 loop : -1.39 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS C1064 PHE 0.012 0.001 PHE C 133 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG B1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 46) link_NAG-ASN : angle 2.36279 ( 138) link_BETA1-4 : bond 0.00339 ( 12) link_BETA1-4 : angle 1.68535 ( 36) hydrogen bonds : bond 0.04080 ( 969) hydrogen bonds : angle 5.99465 ( 2691) SS BOND : bond 0.00236 ( 37) SS BOND : angle 1.31032 ( 74) covalent geometry : bond 0.00229 (23682) covalent geometry : angle 0.56814 (32297) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 27 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: A 1126 CYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8024 (m) REVERT: B 697 MET cc_start: 0.8339 (ptm) cc_final: 0.8050 (ptm) REVERT: B 740 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7838 (tpt) REVERT: B 900 MET cc_start: 0.7177 (mtp) cc_final: 0.6772 (mtm) REVERT: B 1050 MET cc_start: 0.7828 (ptm) cc_final: 0.7454 (ptm) REVERT: C 63 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9066 (p) REVERT: C 239 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6635 (tt0) REVERT: C 328 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.5783 (mmm-85) REVERT: C 523 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8530 (p) REVERT: C 544 ASN cc_start: 0.7133 (OUTLIER) cc_final: 0.6850 (m-40) REVERT: C 546 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6105 (pp) REVERT: C 574 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7102 (t0) REVERT: C 740 MET cc_start: 0.8573 (tpt) cc_final: 0.8283 (tpt) REVERT: C 752 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8657 (tt) REVERT: C 873 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8455 (m-80) outliers start: 47 outliers final: 25 residues processed: 71 average time/residue: 0.3496 time to fit residues: 42.2104 Evaluate side-chains 62 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 25 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 30.0000 chunk 11 optimal weight: 40.0000 chunk 219 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 263 optimal weight: 0.6980 chunk 264 optimal weight: 0.0010 chunk 224 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.038130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.031362 restraints weight = 331033.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.032182 restraints weight = 208811.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.032540 restraints weight = 137694.186| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 23777 Z= 0.114 Angle : 0.578 9.060 32545 Z= 0.294 Chirality : 0.043 0.369 3943 Planarity : 0.004 0.094 4095 Dihedral : 6.079 56.269 4397 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 1.92 % Allowed : 11.15 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.91 (0.16), residues: 2921 helix: 1.07 (0.20), residues: 674 sheet: -0.63 (0.22), residues: 564 loop : -1.33 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS B1058 PHE 0.021 0.001 PHE C 238 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 46) link_NAG-ASN : angle 2.24793 ( 138) link_BETA1-4 : bond 0.00283 ( 12) link_BETA1-4 : angle 1.66841 ( 36) hydrogen bonds : bond 0.04040 ( 969) hydrogen bonds : angle 5.90927 ( 2691) SS BOND : bond 0.00203 ( 37) SS BOND : angle 1.70814 ( 74) covalent geometry : bond 0.00241 (23682) covalent geometry : angle 0.55243 (32297) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 25 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5712 (m-80) REVERT: A 1126 CYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8095 (m) REVERT: B 697 MET cc_start: 0.8352 (ptm) cc_final: 0.8066 (ptm) REVERT: B 740 MET cc_start: 0.8157 (tpt) cc_final: 0.7879 (tpt) REVERT: B 900 MET cc_start: 0.7334 (mtp) cc_final: 0.6953 (mtm) REVERT: B 1050 MET cc_start: 0.7824 (ptm) cc_final: 0.7467 (ptm) REVERT: C 63 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.9111 (p) REVERT: C 328 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.5929 (mmm-85) REVERT: C 523 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8541 (p) REVERT: C 544 ASN cc_start: 0.7220 (OUTLIER) cc_final: 0.6909 (m-40) REVERT: C 546 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6270 (pp) REVERT: C 574 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7075 (t0) REVERT: C 873 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8421 (m-80) outliers start: 45 outliers final: 29 residues processed: 70 average time/residue: 0.3353 time to fit residues: 40.9317 Evaluate side-chains 63 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 25 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1052 PHE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 116 optimal weight: 40.0000 chunk 286 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 chunk 165 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 overall best weight: 3.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.037941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.031158 restraints weight = 332088.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.031823 restraints weight = 206711.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.032261 restraints weight = 148523.275| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23777 Z= 0.137 Angle : 0.579 7.527 32545 Z= 0.294 Chirality : 0.043 0.362 3943 Planarity : 0.004 0.097 4095 Dihedral : 6.007 56.599 4397 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.85 % Favored : 94.01 % Rotamer: Outliers : 1.66 % Allowed : 11.66 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2921 helix: 1.04 (0.20), residues: 673 sheet: -0.72 (0.21), residues: 602 loop : -1.28 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 633 HIS 0.003 0.001 HIS A1048 PHE 0.015 0.001 PHE B 342 TYR 0.016 0.001 TYR A 265 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 46) link_NAG-ASN : angle 2.21085 ( 138) link_BETA1-4 : bond 0.00256 ( 12) link_BETA1-4 : angle 1.73164 ( 36) hydrogen bonds : bond 0.04128 ( 969) hydrogen bonds : angle 5.87502 ( 2691) SS BOND : bond 0.00226 ( 37) SS BOND : angle 1.46412 ( 74) covalent geometry : bond 0.00287 (23682) covalent geometry : angle 0.55570 (32297) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 25 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5743 (m-80) REVERT: A 1126 CYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8238 (m) REVERT: B 697 MET cc_start: 0.8346 (ptm) cc_final: 0.8042 (ptm) REVERT: B 740 MET cc_start: 0.8181 (tpt) cc_final: 0.7885 (tpt) REVERT: B 900 MET cc_start: 0.7400 (mtp) cc_final: 0.7035 (mtm) REVERT: B 1050 MET cc_start: 0.7879 (ptm) cc_final: 0.7540 (ptm) REVERT: C 63 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9122 (p) REVERT: C 523 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8492 (p) REVERT: C 546 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6172 (pp) REVERT: C 574 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.7007 (t0) REVERT: C 697 MET cc_start: 0.7540 (ptm) cc_final: 0.7170 (ptm) REVERT: C 873 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8386 (m-80) outliers start: 39 outliers final: 29 residues processed: 64 average time/residue: 0.3456 time to fit residues: 39.4240 Evaluate side-chains 61 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 25 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 20 optimal weight: 0.0570 chunk 228 optimal weight: 7.9990 chunk 109 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 overall best weight: 5.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** B1048 HIS ** 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 = 0.3532 r_free = 0.3532 target = 0.037585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.030794 restraints weight = 334677.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.031453 restraints weight = 208105.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.031861 restraints weight = 149284.288| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23777 Z= 0.204 Angle : 0.637 7.836 32545 Z= 0.323 Chirality : 0.043 0.367 3943 Planarity : 0.004 0.100 4095 Dihedral : 6.303 56.746 4393 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 1.58 % Allowed : 11.83 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.09 (0.15), residues: 2921 helix: 0.88 (0.20), residues: 671 sheet: -0.93 (0.21), residues: 639 loop : -1.34 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 633 HIS 0.004 0.001 HIS C1048 PHE 0.020 0.002 PHE B 906 TYR 0.018 0.002 TYR B1067 ARG 0.005 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 46) link_NAG-ASN : angle 2.30712 ( 138) link_BETA1-4 : bond 0.00282 ( 12) link_BETA1-4 : angle 1.93021 ( 36) hydrogen bonds : bond 0.04551 ( 969) hydrogen bonds : angle 6.05227 ( 2691) SS BOND : bond 0.00265 ( 37) SS BOND : angle 1.50977 ( 74) covalent geometry : bond 0.00427 (23682) covalent geometry : angle 0.61393 (32297) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 26 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.5709 (m-80) REVERT: A 1126 CYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8330 (m) REVERT: B 697 MET cc_start: 0.8420 (ptm) cc_final: 0.8057 (ptm) REVERT: B 740 MET cc_start: 0.8169 (tpt) cc_final: 0.7818 (tpt) REVERT: B 900 MET cc_start: 0.7578 (mtp) cc_final: 0.7177 (mtm) REVERT: B 1050 MET cc_start: 0.7942 (ptm) cc_final: 0.7559 (ptm) REVERT: C 63 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9141 (p) REVERT: C 523 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8520 (p) REVERT: C 546 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6222 (pp) REVERT: C 574 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6948 (t0) REVERT: C 873 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8536 (m-80) outliers start: 37 outliers final: 29 residues processed: 63 average time/residue: 0.3282 time to fit residues: 36.4648 Evaluate side-chains 61 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 25 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 2 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 284 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 0.0020 chunk 95 optimal weight: 5.9990 overall best weight: 3.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 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 = 0.3545 r_free = 0.3545 target = 0.037828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.031016 restraints weight = 330329.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.031669 restraints weight = 205755.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.032085 restraints weight = 148499.174| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23777 Z= 0.147 Angle : 0.588 7.233 32545 Z= 0.298 Chirality : 0.043 0.347 3943 Planarity : 0.004 0.101 4095 Dihedral : 6.130 57.334 4391 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.89 % Favored : 94.01 % Rotamer: Outliers : 1.58 % Allowed : 11.88 % Favored : 86.55 % 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: -0.97 (0.16), residues: 2921 helix: 1.01 (0.20), residues: 670 sheet: -0.66 (0.21), residues: 615 loop : -1.38 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 633 HIS 0.003 0.001 HIS A1058 PHE 0.017 0.001 PHE B 906 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 46) link_NAG-ASN : angle 2.13777 ( 138) link_BETA1-4 : bond 0.00268 ( 12) link_BETA1-4 : angle 1.76080 ( 36) hydrogen bonds : bond 0.04220 ( 969) hydrogen bonds : angle 5.94448 ( 2691) SS BOND : bond 0.00224 ( 37) SS BOND : angle 1.42996 ( 74) covalent geometry : bond 0.00309 (23682) covalent geometry : angle 0.56633 (32297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6261.09 seconds wall clock time: 110 minutes 17.96 seconds (6617.96 seconds total)