Starting phenix.real_space_refine on Sat Jul 4 21:01:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tpc_26051/07_2026/7tpc_26051.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpc_26051/07_2026/7tpc_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tpc_26051/07_2026/7tpc_26051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpc_26051/07_2026/7tpc_26051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tpc_26051/07_2026/7tpc_26051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpc_26051/07_2026/7tpc_26051.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tpc_26051/07_2026/7tpc_26051.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tpc_26051/07_2026/7tpc_26051.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} 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: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} 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: {'ASN:plan1': 7, 'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 12 Time building chain proxies: 5.71, per 1000 atoms: 0.25 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 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: 0.94 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: 5.80 Time building geometry restraints manager: 2.87 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: 12408 17.78 - 35.57: 945 35.57 - 53.35: 147 53.35 - 71.14: 43 71.14 - 88.92: 32 Dihedral angle restraints: 13575 sinusoidal: 4915 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 13572 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 throug \ h 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 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 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.390 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 14.012 88.923 7870 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG C 44 TYR 0.206 0.026 TYR B 707 PHE 0.126 0.015 PHE B 342 TRP 0.207 0.034 TRP A 886 HIS 0.017 0.004 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01361 / 0.78 (23682) covalent geometry : angle 1.83679 / 1.21 (32297) SS BOND : bond 0.00940 / 0.61 ( 37) SS BOND : angle 2.10401 / 1.41 ( 74) hydrogen bonds : bond 0.15051 / 9.87 ( 969) hydrogen bonds : angle 8.87728 / 6.15 ( 2691) link_BETA1-4 : bond 0.02326 / 1.38 ( 12) link_BETA1-4 : angle 5.09713 / 3.31 ( 36) link_NAG-ASN : bond 0.00936 / 0.58 ( 46) link_NAG-ASN : angle 4.80266 / 3.30 ( 138) *********************** 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 : 0.818 Fit side-chains 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: 0.7687 (mp) REVERT: C 632 THR cc_start: 0.6982 (m) cc_final: 0.6656 (p) REVERT: C 697 MET cc_start: 0.8213 (ptm) cc_final: 0.7907 (ptm) 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: 0.8674 (m-80) REVERT: C 900 MET cc_start: 0.7307 (mpt) cc_final: 0.6571 (mpp) outliers start: 53 outliers final: 13 residues processed: 93 average time/residue: 0.1691 time to fit residues: 25.4056 Evaluate side-chains 45 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN A 935 GLN B 52 GLN B 625 HIS C 99 ASN C 762 GLN C 935 GLN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.038498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.031627 restraints weight = 333312.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.032327 restraints weight = 207469.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.032765 restraints weight = 148384.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.033071 restraints weight = 117284.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.033270 restraints weight = 99519.953| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23777 Z= 0.187 Angle : 0.833 11.072 32545 Z= 0.429 Chirality : 0.048 0.282 3943 Planarity : 0.004 0.061 4095 Dihedral : 8.020 73.524 3191 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.13 % Favored : 93.60 % Rotamer: Outliers : 1.79 % Allowed : 6.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.15), residues: 2921 helix: 0.41 (0.19), residues: 687 sheet: -1.02 (0.22), residues: 502 loop : -1.50 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 237 TYR 0.027 0.002 TYR A 204 PHE 0.027 0.002 PHE B 342 TRP 0.027 0.002 TRP C 633 HIS 0.008 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (23682) covalent geometry : angle 0.78189 / 0.42 (32297) SS BOND : bond 0.00369 / 0.25 ( 37) SS BOND : angle 1.93011 / 1.30 ( 74) hydrogen bonds : bond 0.06075 / 3.99 ( 969) hydrogen bonds : angle 7.07980 / 4.88 ( 2691) link_BETA1-4 : bond 0.00515 / 0.27 ( 12) link_BETA1-4 : angle 2.11807 / 1.33 ( 36) link_NAG-ASN : bond 0.00436 / 0.27 ( 46) link_NAG-ASN : angle 4.18217 / 2.89 ( 138) *********************** 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 74 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 32 time to evaluate : 0.929 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 1050 MET cc_start: 0.8422 (ptm) cc_final: 0.8091 (ptt) REVERT: B 697 MET cc_start: 0.8476 (ptm) cc_final: 0.8191 (ptm) REVERT: B 731 MET cc_start: 0.8940 (mpp) cc_final: 0.8738 (mpp) REVERT: B 900 MET cc_start: 0.7520 (mtp) cc_final: 0.7256 (mtm) REVERT: C 210 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7308 (mp) REVERT: C 523 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8473 (p) REVERT: C 632 THR cc_start: 0.6309 (m) cc_final: 0.5994 (p) REVERT: C 873 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: C 900 MET cc_start: 0.6833 (mpt) cc_final: 0.6540 (mpp) outliers start: 42 outliers final: 22 residues processed: 73 average time/residue: 0.1568 time to fit residues: 19.4337 Evaluate side-chains 52 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 27 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 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 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 112 optimal weight: 0.0060 chunk 157 optimal weight: 0.9980 chunk 258 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 137 optimal weight: 40.0000 chunk 273 optimal weight: 2.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN A 675 GLN A 955 ASN B 641 ASN B 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.038587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.031760 restraints weight = 331510.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.032459 restraints weight = 204510.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.032911 restraints weight = 144831.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.033197 restraints weight = 114172.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.033356 restraints weight = 97115.089| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23777 Z= 0.137 Angle : 0.695 9.978 32545 Z= 0.354 Chirality : 0.046 0.495 3943 Planarity : 0.004 0.070 4095 Dihedral : 6.877 57.462 3186 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.44 % Favored : 93.29 % Rotamer: Outliers : 1.96 % Allowed : 7.45 % Favored : 90.59 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2921 helix: 0.92 (0.20), residues: 664 sheet: -0.78 (0.21), residues: 519 loop : -1.36 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.026 0.002 TYR A 204 PHE 0.020 0.001 PHE B 342 TRP 0.016 0.002 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (23682) covalent geometry : angle 0.66353 / 0.35 (32297) SS BOND : bond 0.00273 / 0.17 ( 37) SS BOND : angle 1.31871 / 0.89 ( 74) hydrogen bonds : bond 0.04912 / 3.23 ( 969) hydrogen bonds : angle 6.48792 / 4.47 ( 2691) link_BETA1-4 : bond 0.00348 / 0.21 ( 12) link_BETA1-4 : angle 1.72058 / 1.09 ( 36) link_NAG-ASN : bond 0.00673 / 0.51 ( 46) link_NAG-ASN : angle 3.02184 / 2.10 ( 138) *********************** 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 75 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 29 time to evaluate : 0.714 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 1126 CYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8231 (m) REVERT: B 697 MET cc_start: 0.8335 (ptm) cc_final: 0.8104 (ptm) REVERT: B 1050 MET cc_start: 0.7899 (ptm) cc_final: 0.7570 (ptp) REVERT: C 328 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.5941 (mmm-85) REVERT: C 523 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8460 (p) REVERT: C 632 THR cc_start: 0.6136 (m) cc_final: 0.5894 (p) REVERT: C 873 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: C 900 MET cc_start: 0.6785 (mpt) cc_final: 0.6135 (mpp) REVERT: C 1032 CYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6545 (m) outliers start: 46 outliers final: 21 residues processed: 74 average time/residue: 0.1292 time to fit residues: 17.0730 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 : 0.868 ------------------------------------------------------------------------------- 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 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 950 ASN Chi-restraints excluded: chain A residue 1126 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 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 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 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 119 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 116 optimal weight: 40.0000 chunk 270 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 130 optimal weight: 50.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 762 GLN B 914 ASN C 493 GLN C 955 ASN C 969 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.037787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.030967 restraints weight = 334254.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.031611 restraints weight = 209727.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.032045 restraints weight = 151363.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.032321 restraints weight = 120157.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.032495 restraints weight = 102506.299| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23777 Z= 0.255 Angle : 0.757 12.412 32545 Z= 0.383 Chirality : 0.046 0.455 3943 Planarity : 0.005 0.075 4095 Dihedral : 6.736 55.488 3177 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.88 % Favored : 92.88 % Rotamer: Outliers : 2.34 % Allowed : 8.85 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 2921 helix: 0.56 (0.20), residues: 677 sheet: -0.87 (0.21), residues: 556 loop : -1.42 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1039 TYR 0.023 0.002 TYR A 204 PHE 0.024 0.002 PHE C1089 TRP 0.015 0.002 TRP B 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (23682) covalent geometry : angle 0.72201 / 0.37 (32297) SS BOND : bond 0.00361 / 0.25 ( 37) SS BOND : angle 2.25399 / 1.54 ( 74) hydrogen bonds : bond 0.05290 / 3.46 ( 969) hydrogen bonds : angle 6.56088 / 4.52 ( 2691) link_BETA1-4 : bond 0.00395 / 0.22 ( 12) link_BETA1-4 : angle 2.03400 / 1.26 ( 36) link_NAG-ASN : bond 0.00709 / 0.50 ( 46) link_NAG-ASN : angle 3.07394 / 2.12 ( 138) *********************** 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 81 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 26 time to evaluate : 0.957 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: 0.6385 (OUTLIER) cc_final: 0.5816 (m-80) REVERT: B 697 MET cc_start: 0.8413 (ptm) cc_final: 0.8057 (ptm) REVERT: B 738 CYS cc_start: 0.4647 (OUTLIER) cc_final: 0.4415 (p) REVERT: B 1050 MET cc_start: 0.7889 (ptm) cc_final: 0.7488 (ptm) REVERT: C 328 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6254 (mmm-85) REVERT: C 523 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8532 (p) REVERT: C 546 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6447 (pp) REVERT: C 632 THR cc_start: 0.5993 (m) cc_final: 0.5749 (p) REVERT: C 873 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: C 900 MET cc_start: 0.6964 (mpt) cc_final: 0.6457 (mpp) outliers start: 55 outliers final: 26 residues processed: 79 average time/residue: 0.1452 time to fit residues: 20.1062 Evaluate side-chains 58 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 26 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 547 THR 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 736 VAL Chi-restraints excluded: chain B residue 738 CYS 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 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 23 optimal weight: 5.9990 chunk 197 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 292 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 134 optimal weight: 50.0000 chunk 274 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 207 HIS B 762 GLN C 519 HIS C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.037848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.031006 restraints weight = 332050.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.031651 restraints weight = 208833.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.032086 restraints weight = 150758.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.032375 restraints weight = 119452.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.032564 restraints weight = 101588.911| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23777 Z= 0.184 Angle : 0.678 11.640 32545 Z= 0.345 Chirality : 0.044 0.415 3943 Planarity : 0.004 0.081 4095 Dihedral : 6.449 56.096 3177 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 1.75 % Allowed : 10.09 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 2921 helix: 0.77 (0.20), residues: 667 sheet: -0.78 (0.21), residues: 552 loop : -1.45 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.019 0.002 TYR A 204 PHE 0.019 0.002 PHE B 342 TRP 0.018 0.002 TRP A 104 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (23682) covalent geometry : angle 0.64689 / 0.34 (32297) SS BOND : bond 0.00252 / 0.17 ( 37) SS BOND : angle 2.14732 / 1.43 ( 74) hydrogen bonds : bond 0.04776 / 3.13 ( 969) hydrogen bonds : angle 6.36553 / 4.38 ( 2691) link_BETA1-4 : bond 0.00307 / 0.17 ( 12) link_BETA1-4 : angle 1.78719 / 1.14 ( 36) link_NAG-ASN : bond 0.00455 / 0.32 ( 46) link_NAG-ASN : angle 2.65510 / 1.83 ( 138) *********************** 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 67 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 26 time to evaluate : 0.868 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: 0.6385 (OUTLIER) cc_final: 0.5850 (m-80) REVERT: A 1050 MET cc_start: 0.8977 (ptt) cc_final: 0.8659 (ptm) REVERT: A 1126 CYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8246 (m) REVERT: B 697 MET cc_start: 0.8447 (ptm) cc_final: 0.8091 (ptm) REVERT: B 1050 MET cc_start: 0.7972 (ptm) cc_final: 0.7732 (ptm) REVERT: C 63 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9178 (p) REVERT: C 328 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6099 (mmm-85) REVERT: C 523 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8519 (p) REVERT: C 546 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6203 (pp) REVERT: C 873 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8529 (m-80) outliers start: 41 outliers final: 24 residues processed: 66 average time/residue: 0.1494 time to fit residues: 17.3493 Evaluate side-chains 56 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 25 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 1126 CYS Chi-restraints excluded: chain B residue 90 VAL 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 912 THR Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 62 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 128 optimal weight: 50.0000 chunk 54 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 287 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 196 ASN C 644 GLN C 955 ASN C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.037831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.030988 restraints weight = 334847.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.031648 restraints weight = 208690.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.032064 restraints weight = 149403.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.032348 restraints weight = 119008.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.032507 restraints weight = 101370.209| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23777 Z= 0.171 Angle : 0.645 8.273 32545 Z= 0.326 Chirality : 0.044 0.321 3943 Planarity : 0.004 0.086 4095 Dihedral : 6.216 56.179 3177 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.54 % Favored : 93.26 % Rotamer: Outliers : 1.79 % Allowed : 10.30 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 2921 helix: 0.81 (0.20), residues: 670 sheet: -0.74 (0.22), residues: 544 loop : -1.39 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.022 0.002 TYR A 266 PHE 0.017 0.001 PHE B 342 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (23682) covalent geometry : angle 0.62040 / 0.32 (32297) SS BOND : bond 0.00276 / 0.19 ( 37) SS BOND : angle 1.58699 / 1.06 ( 74) hydrogen bonds : bond 0.04603 / 3.00 ( 969) hydrogen bonds : angle 6.23415 / 4.29 ( 2691) link_BETA1-4 : bond 0.00262 / 0.15 ( 12) link_BETA1-4 : angle 1.76915 / 1.12 ( 36) link_NAG-ASN : bond 0.00491 / 0.36 ( 46) link_NAG-ASN : angle 2.41675 / 1.66 ( 138) *********************** 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 67 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 25 time to evaluate : 1.133 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: 0.6422 (OUTLIER) cc_final: 0.5729 (m-80) REVERT: A 1126 CYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8157 (m) REVERT: B 298 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: B 697 MET cc_start: 0.8402 (ptm) cc_final: 0.8045 (ptm) REVERT: B 740 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7965 (tpt) REVERT: B 1050 MET cc_start: 0.7972 (ptm) cc_final: 0.7583 (ptm) REVERT: C 63 THR cc_start: 0.9428 (OUTLIER) cc_final: 0.9171 (p) REVERT: C 328 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6096 (mmm-85) REVERT: C 523 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8510 (p) REVERT: C 574 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6949 (t0) REVERT: C 873 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8553 (m-80) outliers start: 42 outliers final: 26 residues processed: 66 average time/residue: 0.1478 time to fit residues: 17.2429 Evaluate side-chains 60 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 25 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 298 GLU 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 B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 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 574 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 150 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 176 optimal weight: 0.6980 chunk 250 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.037740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.030907 restraints weight = 333943.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.031561 restraints weight = 208058.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.031990 restraints weight = 149220.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.032265 restraints weight = 118041.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.032454 restraints weight = 100800.727| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23777 Z= 0.181 Angle : 0.642 8.996 32545 Z= 0.324 Chirality : 0.044 0.378 3943 Planarity : 0.004 0.090 4095 Dihedral : 6.136 56.517 3177 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.74 % Favored : 93.08 % Rotamer: Outliers : 2.09 % Allowed : 10.47 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 2921 helix: 0.84 (0.20), residues: 666 sheet: -0.89 (0.22), residues: 558 loop : -1.38 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.018 0.002 TYR A 204 PHE 0.017 0.001 PHE B 342 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (23682) covalent geometry : angle 0.61778 / 0.32 (32297) SS BOND : bond 0.00266 / 0.18 ( 37) SS BOND : angle 1.45242 / 0.99 ( 74) hydrogen bonds : bond 0.04590 / 2.99 ( 969) hydrogen bonds : angle 6.21983 / 4.28 ( 2691) link_BETA1-4 : bond 0.00273 / 0.16 ( 12) link_BETA1-4 : angle 1.76755 / 1.12 ( 36) link_NAG-ASN : bond 0.00498 / 0.33 ( 46) link_NAG-ASN : angle 2.46389 / 1.70 ( 138) *********************** 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: 49 poor density : 25 time to evaluate : 0.856 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: 0.6450 (OUTLIER) cc_final: 0.5746 (m-80) REVERT: A 1126 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8082 (m) REVERT: B 298 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: B 697 MET cc_start: 0.8425 (ptm) cc_final: 0.8043 (ptm) REVERT: B 740 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7909 (tpt) REVERT: B 1050 MET cc_start: 0.7968 (ptm) cc_final: 0.7594 (ptm) REVERT: C 63 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9180 (p) REVERT: C 328 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.5942 (mmm-85) REVERT: C 523 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8497 (p) REVERT: C 546 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6265 (pp) REVERT: C 574 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6901 (t0) REVERT: C 873 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8551 (m-80) outliers start: 49 outliers final: 28 residues processed: 71 average time/residue: 0.1374 time to fit residues: 17.0153 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 : 0.745 ------------------------------------------------------------------------------- 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 547 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 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 298 GLU 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 B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 328 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 592 PHE Chi-restraints excluded: chain C residue 611 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 283 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 148 optimal weight: 30.0000 chunk 279 optimal weight: 5.9990 chunk 7 optimal weight: 40.0000 chunk 293 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN ** A 901 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 = 0.3538 r_free = 0.3538 target = 0.037709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.030883 restraints weight = 330751.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.031545 restraints weight = 206470.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.031959 restraints weight = 147748.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.032245 restraints weight = 117519.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.032431 restraints weight = 100295.150| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23777 Z= 0.170 Angle : 0.624 8.060 32545 Z= 0.315 Chirality : 0.044 0.371 3943 Planarity : 0.004 0.094 4095 Dihedral : 5.990 56.772 3175 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.71 % Favored : 93.15 % Rotamer: Outliers : 1.92 % Allowed : 10.86 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 2921 helix: 0.85 (0.20), residues: 671 sheet: -0.72 (0.22), residues: 561 loop : -1.40 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.016 0.001 TYR A 204 PHE 0.014 0.001 PHE B 342 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (23682) covalent geometry : angle 0.60105 / 0.31 (32297) SS BOND : bond 0.00265 / 0.17 ( 37) SS BOND : angle 1.43280 / 0.97 ( 74) hydrogen bonds : bond 0.04462 / 2.91 ( 969) hydrogen bonds : angle 6.14298 / 4.22 ( 2691) link_BETA1-4 : bond 0.00250 / 0.14 ( 12) link_BETA1-4 : angle 1.71508 / 1.10 ( 36) link_NAG-ASN : bond 0.00405 / 0.29 ( 46) link_NAG-ASN : angle 2.35339 / 1.61 ( 138) *********************** 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 : 0.862 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: 0.6457 (OUTLIER) cc_final: 0.5750 (m-80) REVERT: A 1126 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7995 (m) REVERT: B 298 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: B 697 MET cc_start: 0.8412 (ptm) cc_final: 0.8042 (ptm) REVERT: B 740 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7875 (tpt) REVERT: B 1050 MET cc_start: 0.7920 (ptm) cc_final: 0.7546 (ptm) REVERT: C 63 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.9162 (p) REVERT: C 523 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8481 (p) REVERT: C 546 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6258 (pp) REVERT: C 574 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6936 (t0) REVERT: C 873 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: C 1050 MET cc_start: 0.8853 (ptt) cc_final: 0.8404 (ptt) outliers start: 45 outliers final: 29 residues processed: 68 average time/residue: 0.1162 time to fit residues: 14.2833 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 : 0.779 ------------------------------------------------------------------------------- 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 739 THR Chi-restraints excluded: chain A residue 980 ILE 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 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 298 GLU 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 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL 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 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 611 LEU 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 132 optimal weight: 0.0070 chunk 81 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 7 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 211 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 222 optimal weight: 0.0040 chunk 61 optimal weight: 4.9990 overall best weight: 2.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 239 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.037930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.031096 restraints weight = 331470.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.031760 restraints weight = 205499.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.032177 restraints weight = 147272.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.032462 restraints weight = 117498.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.032652 restraints weight = 100195.719| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23777 Z= 0.129 Angle : 0.581 7.263 32545 Z= 0.294 Chirality : 0.043 0.350 3943 Planarity : 0.004 0.097 4095 Dihedral : 5.739 57.287 3171 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.23 % Favored : 93.67 % Rotamer: Outliers : 1.79 % Allowed : 10.98 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2921 helix: 1.00 (0.20), residues: 667 sheet: -0.60 (0.22), residues: 562 loop : -1.31 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.016 0.001 TYR B1067 PHE 0.013 0.001 PHE B 342 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (23682) covalent geometry : angle 0.56011 / 0.29 (32297) SS BOND : bond 0.00210 / 0.13 ( 37) SS BOND : angle 1.31615 / 0.89 ( 74) hydrogen bonds : bond 0.04153 / 2.72 ( 969) hydrogen bonds : angle 5.97841 / 4.11 ( 2691) link_BETA1-4 : bond 0.00274 / 0.16 ( 12) link_BETA1-4 : angle 1.56899 / 1.02 ( 36) link_NAG-ASN : bond 0.00336 / 0.24 ( 46) link_NAG-ASN : angle 2.17348 / 1.50 ( 138) *********************** 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 68 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 26 time to evaluate : 0.900 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: 0.6405 (OUTLIER) cc_final: 0.5737 (m-80) REVERT: A 1126 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7950 (m) REVERT: B 298 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: B 697 MET cc_start: 0.8327 (ptm) cc_final: 0.8037 (ptm) REVERT: B 740 MET cc_start: 0.8157 (tpt) cc_final: 0.7867 (tpt) REVERT: B 1050 MET cc_start: 0.7832 (ptm) cc_final: 0.7439 (ptm) REVERT: C 63 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9109 (p) REVERT: C 523 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8574 (p) REVERT: C 546 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6232 (pp) REVERT: C 574 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6957 (t0) REVERT: C 873 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8497 (m-80) outliers start: 42 outliers final: 30 residues processed: 67 average time/residue: 0.1369 time to fit residues: 16.2123 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 : 0.846 ------------------------------------------------------------------------------- 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 739 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 298 GLU 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 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 B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL 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 592 PHE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 869 MET 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 160 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 209 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 225 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.037688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.030873 restraints weight = 332117.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.031531 restraints weight = 206266.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.031937 restraints weight = 147927.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.032219 restraints weight = 118123.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.032411 restraints weight = 100676.277| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23777 Z= 0.186 Angle : 0.618 8.183 32545 Z= 0.312 Chirality : 0.043 0.346 3943 Planarity : 0.004 0.100 4095 Dihedral : 5.791 57.557 3171 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.02 % Favored : 92.88 % Rotamer: Outliers : 1.83 % Allowed : 10.86 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2921 helix: 0.91 (0.20), residues: 672 sheet: -0.83 (0.21), residues: 597 loop : -1.36 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.017 0.002 TYR B1067 PHE 0.016 0.001 PHE B 201 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (23682) covalent geometry : angle 0.59673 / 0.31 (32297) SS BOND : bond 0.00261 / 0.17 ( 37) SS BOND : angle 1.34924 / 0.91 ( 74) hydrogen bonds : bond 0.04427 / 2.89 ( 969) hydrogen bonds : angle 6.05594 / 4.17 ( 2691) link_BETA1-4 : bond 0.00271 / 0.15 ( 12) link_BETA1-4 : angle 1.73724 / 1.11 ( 36) link_NAG-ASN : bond 0.00389 / 0.26 ( 46) link_NAG-ASN : angle 2.22175 / 1.52 ( 138) ********************** 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 68 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 25 time to evaluate : 0.926 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: 0.6421 (OUTLIER) cc_final: 0.5685 (m-80) REVERT: A 1126 CYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8095 (m) REVERT: B 298 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: B 697 MET cc_start: 0.8382 (ptm) cc_final: 0.8061 (ptm) REVERT: B 740 MET cc_start: 0.8224 (tpt) cc_final: 0.7925 (tpt) REVERT: B 1050 MET cc_start: 0.7923 (ptm) cc_final: 0.7690 (ptm) REVERT: C 63 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9149 (p) REVERT: C 523 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8610 (p) REVERT: C 546 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6220 (pp) REVERT: C 574 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6955 (t0) REVERT: C 873 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8562 (m-80) outliers start: 43 outliers final: 33 residues processed: 67 average time/residue: 0.1391 time to fit residues: 16.7230 Evaluate side-chains 66 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 25 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 739 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 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 298 GLU 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 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 B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL 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 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 869 MET 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 202 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 283 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.037886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.031048 restraints weight = 330586.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.031705 restraints weight = 205286.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.032145 restraints weight = 147359.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.032429 restraints weight = 116660.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.032608 restraints weight = 99264.663| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23777 Z= 0.138 Angle : 0.582 7.207 32545 Z= 0.294 Chirality : 0.043 0.336 3943 Planarity : 0.004 0.102 4095 Dihedral : 5.688 57.916 3171 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.23 % Favored : 93.67 % Rotamer: Outliers : 1.83 % Allowed : 10.90 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.16), residues: 2921 helix: 0.99 (0.20), residues: 672 sheet: -0.60 (0.22), residues: 583 loop : -1.34 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE B 201 TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (23682) covalent geometry : angle 0.56139 / 0.29 (32297) SS BOND : bond 0.00217 / 0.14 ( 37) SS BOND : angle 1.30483 / 0.88 ( 74) hydrogen bonds : bond 0.04173 / 2.73 ( 969) hydrogen bonds : angle 5.96801 / 4.11 ( 2691) link_BETA1-4 : bond 0.00283 / 0.16 ( 12) link_BETA1-4 : angle 1.59644 / 1.03 ( 36) link_NAG-ASN : bond 0.00327 / 0.23 ( 46) link_NAG-ASN : angle 2.13761 / 1.46 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3382.18 seconds wall clock time: 59 minutes 44.87 seconds (3584.87 seconds total)