Starting phenix.real_space_refine on Fri Mar 6 19:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9n_31033/03_2026/7e9n_31033.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9n_31033/03_2026/7e9n_31033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e9n_31033/03_2026/7e9n_31033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9n_31033/03_2026/7e9n_31033.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e9n_31033/03_2026/7e9n_31033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9n_31033/03_2026/7e9n_31033.map" } resolution = 3.69 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= 0.000 sd= 0.048 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 145 5.16 5 C 21280 2.51 5 N 5554 2.21 5 O 6540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 207 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33519 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7805 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7535 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 52, 'TRANS': 924} Chain breaks: 11 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 4, 'ARG:plan': 3, 'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "X" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1655 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1653 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1664 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.77, per 1000 atoms: 0.23 Number of scatterers: 33519 At special positions: 0 Unit cell: (169.725, 196.005, 227.76, 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 145 16.00 O 6540 8.00 N 5554 7.00 C 21280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 199 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 157 " - pdb=" SG CYS P 213 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS X 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.04 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 NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8026 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 67 sheets defined 18.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.245A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.537A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.910A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.377A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.557A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.568A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.554A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.812A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.284A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.230A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.925A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.604A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.460A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.623A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.642A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.148A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.604A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.646A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.325A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 336 through 341 removed outlier: 3.760A pdb=" N GLY C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 408 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.731A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 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 760 through 783 removed outlier: 4.319A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.873A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.595A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.734A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.504A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.633A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.913A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.439A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.804A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 88 removed outlier: 3.749A pdb=" N VAL O 88 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 131 Processing helix chain 'O' and resid 188 through 194 removed outlier: 3.650A pdb=" N GLU O 192 " --> pdb=" O LYS O 188 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS O 194 " --> pdb=" O ASP O 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.224A pdb=" N ASP P 31 " --> pdb=" O THR P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 65 removed outlier: 3.506A pdb=" N VAL P 64 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS P 65 " --> pdb=" O ASP P 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 65' Processing helix chain 'P' and resid 173 through 175 No H-bonds generated for 'chain 'P' and resid 173 through 175' Processing helix chain 'X' and resid 84 through 88 removed outlier: 3.985A pdb=" N VAL X 88 " --> pdb=" O ALA X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 126 through 131 Processing helix chain 'X' and resid 188 through 194 removed outlier: 3.843A pdb=" N GLU X 192 " --> pdb=" O LYS X 188 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS X 194 " --> pdb=" O ASP X 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 32 removed outlier: 4.134A pdb=" N ASP Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 28 through 32' Processing helix chain 'Y' and resid 61 through 65 removed outlier: 4.043A pdb=" N LYS Y 65 " --> pdb=" O ASP Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 175 No H-bonds generated for 'chain 'Y' and resid 173 through 175' Processing helix chain 'Y' and resid 204 through 206 No H-bonds generated for 'chain 'Y' and resid 204 through 206' Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.112A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.816A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.912A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.620A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.750A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.541A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.051A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AB2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB3, first strand: chain 'B' and resid 1094 through 1098 removed outlier: 3.593A pdb=" N ASN B1098 " --> pdb=" O HIS B1101 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B1101 " --> pdb=" O ASN B1098 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.067A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.575A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AB8, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.762A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.558A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AC3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.632A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.525A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AC6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.193A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.626A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC9, first strand: chain 'A' and resid 1094 through 1098 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.726A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.173A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.723A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.674A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.668A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.275A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.551A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.939A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.122A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'O' and resid 50 through 53 removed outlier: 6.487A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 119 through 123 Processing sheet with id=AE9, first strand: chain 'O' and resid 150 through 155 Processing sheet with id=AF1, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'P' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'P' and resid 46 through 51 removed outlier: 6.915A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET P 34 " --> pdb=" O GLY P 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 137 through 141 removed outlier: 6.444A pdb=" N TYR P 193 " --> pdb=" O ASP P 161 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N SER P 194 " --> pdb=" O ALA P 185 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA P 185 " --> pdb=" O SER P 194 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER P 196 " --> pdb=" O PHE P 183 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 168 through 171 Processing sheet with id=AF6, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'X' and resid 50 through 53 removed outlier: 6.446A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 119 through 123 Processing sheet with id=AF9, first strand: chain 'X' and resid 150 through 154 Processing sheet with id=AG1, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'Y' and resid 57 through 59 removed outlier: 7.034A pdb=" N GLY Y 50 " --> pdb=" O ILE Y 58 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET Y 34 " --> pdb=" O GLY Y 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 137 through 141 removed outlier: 6.558A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER Y 194 " --> pdb=" O ALA Y 185 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA Y 185 " --> pdb=" O SER Y 194 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER Y 196 " --> pdb=" O PHE Y 183 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE Y 183 " --> pdb=" O SER Y 196 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 168 through 171 Processing sheet with id=AG6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.562A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.920A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.771A pdb=" N VAL L 155 " --> pdb=" O ALA L 158 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.666A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.009A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 167 through 171 1290 hydrogen bonds defined for protein. 3411 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: 7.87 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5551 1.32 - 1.45: 10002 1.45 - 1.59: 18533 1.59 - 1.72: 0 1.72 - 1.86: 186 Bond restraints: 34272 Sorted by residual: bond pdb=" C7 NAG A1305 " pdb=" N2 NAG A1305 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C7 NAG A1306 " pdb=" N2 NAG A1306 " ideal model delta sigma weight residual 1.346 1.460 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C7 NAG A1309 " pdb=" N2 NAG A1309 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C7 NAG C1303 " pdb=" N2 NAG C1303 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 34267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 44645 2.07 - 4.15: 1722 4.15 - 6.22: 260 6.22 - 8.29: 31 8.29 - 10.37: 11 Bond angle restraints: 46669 Sorted by residual: angle pdb=" N GLN C 913 " pdb=" CA GLN C 913 " pdb=" C GLN C 913 " ideal model delta sigma weight residual 112.89 121.03 -8.14 1.24e+00 6.50e-01 4.31e+01 angle pdb=" N GLN A 913 " pdb=" CA GLN A 913 " pdb=" C GLN A 913 " ideal model delta sigma weight residual 112.23 118.92 -6.69 1.26e+00 6.30e-01 2.82e+01 angle pdb=" CA GLY Y 116 " pdb=" C GLY Y 116 " pdb=" O GLY Y 116 " ideal model delta sigma weight residual 122.59 118.33 4.26 1.04e+00 9.25e-01 1.68e+01 angle pdb=" N GLU B 281 " pdb=" CA GLU B 281 " pdb=" C GLU B 281 " ideal model delta sigma weight residual 111.33 116.26 -4.93 1.21e+00 6.83e-01 1.66e+01 angle pdb=" N GLU A 406 " pdb=" CA GLU A 406 " pdb=" C GLU A 406 " ideal model delta sigma weight residual 113.15 108.49 4.66 1.19e+00 7.06e-01 1.53e+01 ... (remaining 46664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 19592 24.42 - 48.84: 1017 48.84 - 73.26: 119 73.26 - 97.68: 35 97.68 - 122.10: 20 Dihedral angle restraints: 20783 sinusoidal: 8302 harmonic: 12481 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 2.74 -88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.87 -84.87 1 1.00e+01 1.00e-02 8.74e+01 ... (remaining 20780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4979 0.104 - 0.208: 404 0.208 - 0.313: 14 0.313 - 0.417: 1 0.417 - 0.521: 2 Chirality restraints: 5400 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.17e+00 ... (remaining 5397 not shown) Planarity restraints: 6038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 224 " -0.064 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO C 225 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Y 163 " 0.061 5.00e-02 4.00e+02 9.08e-02 1.32e+01 pdb=" N PRO Y 164 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO Y 164 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO Y 164 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 84 " -0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO B 85 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " -0.046 5.00e-02 4.00e+02 ... (remaining 6035 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4874 2.75 - 3.29: 32435 3.29 - 3.83: 52034 3.83 - 4.36: 60246 4.36 - 4.90: 106050 Nonbonded interactions: 255639 Sorted by model distance: nonbonded pdb=" O GLY C1085 " pdb=" N CYS C1126 " model vdw 2.217 3.120 nonbonded pdb=" O PHE C 106 " pdb=" OG SER C 116 " model vdw 2.223 3.040 nonbonded pdb=" O ASN B 422 " pdb=" NH2 ARG B 454 " model vdw 2.224 3.120 nonbonded pdb=" NH1 ARG B 34 " pdb=" OE2 GLU B 191 " model vdw 2.231 3.120 nonbonded pdb=" O GLN Y 39 " pdb=" N LEU Y 93 " model vdw 2.231 3.120 ... (remaining 255634 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 213 or (resid 214 and (name N or name CA or nam \ e C or name O or name CB )) or resid 215 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 377 or (resid 3 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 379 through \ 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) or r \ esid 529 through 723 or (resid 724 and (name N or name CA or name C or name O or \ name CB )) or resid 725 through 813 or (resid 814 and (name N or name CA or nam \ e C or name O or name CB )) or resid 815 through 1309)) selection = (chain 'B' and (resid 27 through 331 or (resid 332 through 333 and (name N or na \ me CA or name C or name O or name CB )) or resid 334 through 368 or (resid 369 a \ nd (name N or name CA or name C or name O or name CB )) or resid 370 through 402 \ or (resid 403 and (name N or name CA or name C or name O or name CB )) or resid \ 404 or (resid 405 through 408 and (name N or name CA or name C or name O or nam \ e CB )) or resid 409 through 413 or (resid 414 through 415 and (name N or name C \ A or name C or name O or name CB )) or resid 416 or (resid 417 and (name N or na \ me CA or name C or name O or name CB )) or resid 418 through 419 or (resid 420 a \ nd (name N or name CA or name C or name O or name CB )) or resid 421 through 423 \ or (resid 424 and (name N or name CA or name C or name O or name CB )) or resid \ 425 through 440 or (resid 441 and (name N or name CA or name C or name O or nam \ e CB )) or resid 442 through 443 or (resid 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or (resid 460 and (name N or name CA or \ name C or name O or name CB )) or resid 461 through 464 or (resid 465 and (name \ N or name CA or name C or name O or name CB )) or resid 466 or (resid 467 throug \ h 469 and (name N or name CA or name C or name O or name CB )) or resid 470 or ( \ resid 471 through 473 and (name N or name CA or name C or name O or name CB )) o \ r resid 487 through 497 or (resid 498 and (name N or name CA or name C or name O \ or name CB )) or resid 499 through 500 or resid 503 through 504 or (resid 505 a \ nd (name N or name CA or name C or name O or name CB )) or resid 506 through 515 \ or (resid 516 and (name N or name CA or name C or name O or name CB )) or resid \ 517 through 518 or (resid 519 through 520 and (name N or name CA or name C or n \ ame O or name CB )) or resid 521 through 723 or (resid 724 and (name N or name C \ A or name C or name O or name CB )) or resid 725 through 1309)) selection = (chain 'C' and (resid 27 through 213 or (resid 214 and (name N or name CA or nam \ e C or name O or name CB )) or resid 215 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 331 or (resid 3 \ 32 through 333 and (name N or name CA or name C or name O or name CB )) or resid \ 334 through 368 or (resid 369 and (name N or name CA or name C or name O or nam \ e CB )) or resid 370 through 377 or (resid 378 and (name N or name CA or name C \ or name O or name CB )) or resid 379 through 402 or (resid 403 and (name N or na \ me CA or name C or name O or name CB )) or resid 404 or (resid 405 through 408 a \ nd (name N or name CA or name C or name O or name CB )) or resid 409 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 or (resid 417 and (name N or name CA or name C or name O or nam \ e CB )) or resid 418 through 419 or (resid 420 and (name N or name CA or name C \ or name O or name CB )) or resid 421 through 423 or (resid 424 and (name N or na \ me CA or name C or name O or name CB )) or resid 425 through 440 or (resid 441 a \ nd (name N or name CA or name C or name O or name CB )) or resid 442 through 443 \ or (resid 449 and (name N or name CA or name C or name O or name CB )) or resid \ 450 through 453 or (resid 454 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 460 and (name N or name CA or name C or name O or name CB )) o \ r resid 461 through 464 or (resid 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 or (resid 467 through 469 and (name N or name CA or \ name C or name O or name CB )) or resid 470 or (resid 471 through 473 and (name \ N or name CA or name C or name O or name CB )) or resid 487 through 497 or (resi \ d 498 and (name N or name CA or name C or name O or name CB )) or resid 499 thro \ ugh 500 or resid 503 through 504 or (resid 505 and (name N or name CA or name C \ or name O or name CB )) or resid 506 through 515 or (resid 516 and (name N or na \ me CA or name C or name O or name CB )) or resid 517 through 518 or (resid 519 t \ hrough 520 and (name N or name CA or name C or name O or name CB )) or resid 521 \ through 527 or (resid 528 and (name N or name CA or name C or name O or name CB \ )) or resid 529 through 813 or (resid 814 and (name N or name CA or name C or n \ ame O or name CB )) or resid 815 through 1309)) } ncs_group { reference = (chain 'H' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 116 or (resid 117 and (name N or \ name CA or name C or name O or name CB )) or resid 118 through 198 or (resid 199 \ and (name N or name CA or name C or name O or name CB )) or resid 200 through 2 \ 32)) selection = (chain 'P' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 116 or (resid 117 and (name N or \ name CA or name C or name O or name CB )) or resid 118 through 198 or (resid 199 \ and (name N or name CA or name C or name O or name CB )) or resid 200 through 2 \ 08 or (resid 209 and (name N or name CA or name C or name O or name CB )) or res \ id 210 through 232)) selection = (chain 'Y' and (resid 1 through 208 or (resid 209 and (name N or name CA or name \ C or name O or name CB )) or resid 210 through 232)) } ncs_group { reference = (chain 'L' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 127 or (resid 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 146 or (resid 147 a \ nd (name N or name CA or name C or name O or name CB )) or resid 148 through 192 \ or (resid 193 and (name N or name CA or name C or name O or name CB )) or resid \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 218)) selection = (chain 'O' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 78 or (resid 79 and (name N or name \ CA or name C or name O or name CB )) or resid 80 through 146 or (resid 147 and \ (name N or name CA or name C or name O or name CB )) or resid 148 through 192 or \ (resid 193 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 4 or (resid 195 and (name N or name CA or name C or name O or name CB )) or resi \ d 196 through 218)) selection = (chain 'X' and (resid 1 through 78 or (resid 79 and (name N or name CA or name C \ or name O or name CB )) or resid 80 through 127 or (resid 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 218)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.630 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.009 0.116 34347 Z= 0.451 Angle : 0.989 68.856 46846 Z= 0.543 Chirality : 0.058 0.521 5400 Planarity : 0.006 0.100 6011 Dihedral : 14.954 122.100 12613 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.05 % Allowed : 1.06 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -2.35 (0.12), residues: 4233 helix: -0.15 (0.20), residues: 641 sheet: -1.09 (0.14), residues: 1287 loop : -2.32 (0.12), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 905 TYR 0.046 0.002 TYR A 904 PHE 0.055 0.003 PHE B 906 TRP 0.026 0.002 TRP Y 171 HIS 0.023 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00930 (34272) covalent geometry : angle 0.92111 (46669) SS BOND : bond 0.00722 ( 48) SS BOND : angle 7.32130 ( 96) hydrogen bonds : bond 0.13536 ( 1286) hydrogen bonds : angle 7.57074 ( 3411) link_NAG-ASN : bond 0.00620 ( 27) link_NAG-ASN : angle 3.61082 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.8901 (mmm) cc_final: 0.8539 (tpp) REVERT: B 1050 MET cc_start: 0.7563 (mtp) cc_final: 0.7334 (mtp) REVERT: O 14 THR cc_start: 0.7970 (m) cc_final: 0.7638 (t) REVERT: P 102 MET cc_start: 0.8300 (tpt) cc_final: 0.7745 (tpt) REVERT: X 143 ASN cc_start: 0.9112 (m-40) cc_final: 0.8825 (t0) REVERT: X 174 LYS cc_start: 0.6613 (pttm) cc_final: 0.6101 (pttm) REVERT: L 4 MET cc_start: 0.3287 (mtt) cc_final: 0.1804 (mpp) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.2356 time to fit residues: 76.4374 Evaluate side-chains 96 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 690 GLN B 901 GLN A 343 ASN A 901 GLN C 360 ASN C 751 ASN C 901 GLN C1088 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 194 HIS ** O 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 95 GLN Y 1 GLN Y 3 GLN H 82 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.087082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.059064 restraints weight = 215098.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.059054 restraints weight = 110624.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.058934 restraints weight = 71376.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.059337 restraints weight = 48796.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.059433 restraints weight = 37894.916| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34347 Z= 0.184 Angle : 0.662 14.862 46846 Z= 0.336 Chirality : 0.046 0.373 5400 Planarity : 0.005 0.065 6011 Dihedral : 8.739 114.772 5156 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.65 % Allowed : 7.80 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.73 (0.13), residues: 4233 helix: 0.94 (0.20), residues: 648 sheet: -0.89 (0.14), residues: 1283 loop : -1.98 (0.12), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 66 TYR 0.022 0.002 TYR C 904 PHE 0.031 0.002 PHE B 329 TRP 0.014 0.002 TRP B 104 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00416 (34272) covalent geometry : angle 0.64313 (46669) SS BOND : bond 0.00485 ( 48) SS BOND : angle 1.43068 ( 96) hydrogen bonds : bond 0.04838 ( 1286) hydrogen bonds : angle 5.94209 ( 3411) link_NAG-ASN : bond 0.00560 ( 27) link_NAG-ASN : angle 3.61264 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8268 (mtm) REVERT: B 902 MET cc_start: 0.8877 (mmm) cc_final: 0.8267 (tpp) REVERT: B 1050 MET cc_start: 0.8101 (mtp) cc_final: 0.7487 (mtp) REVERT: A 1050 MET cc_start: 0.7653 (mtp) cc_final: 0.7410 (mtp) REVERT: C 429 PHE cc_start: 0.8033 (t80) cc_final: 0.7789 (t80) REVERT: O 14 THR cc_start: 0.8216 (m) cc_final: 0.7998 (t) REVERT: O 82 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7558 (mtt-85) REVERT: O 147 ARG cc_start: 0.8741 (ttp-110) cc_final: 0.8498 (tpt90) REVERT: P 163 PHE cc_start: 0.8491 (t80) cc_final: 0.8238 (t80) REVERT: X 82 ARG cc_start: 0.8823 (mtp85) cc_final: 0.8504 (ptp-110) REVERT: X 95 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8045 (pp30) REVERT: X 112 LYS cc_start: 0.8643 (tptt) cc_final: 0.8430 (tptt) REVERT: X 174 LYS cc_start: 0.7937 (pttm) cc_final: 0.7677 (pttm) REVERT: Y 90 ASP cc_start: 0.7402 (m-30) cc_final: 0.7073 (m-30) outliers start: 24 outliers final: 12 residues processed: 125 average time/residue: 0.2305 time to fit residues: 46.2236 Evaluate side-chains 109 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain X residue 54 TYR Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain Y residue 106 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 273 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 256 optimal weight: 4.9990 chunk 342 optimal weight: 40.0000 chunk 227 optimal weight: 20.0000 chunk 275 optimal weight: 2.9990 overall best weight: 4.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A1010 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN O 58 ASN P 3 GLN P 181 HIS X 95 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.085563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056155 restraints weight = 209277.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.052235 restraints weight = 93017.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.052588 restraints weight = 58754.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.052813 restraints weight = 42840.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.053012 restraints weight = 36070.469| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 34347 Z= 0.220 Angle : 0.654 14.313 46846 Z= 0.333 Chirality : 0.046 0.411 5400 Planarity : 0.005 0.063 6011 Dihedral : 7.951 118.794 5156 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.97 % Allowed : 11.67 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.55 (0.13), residues: 4233 helix: 1.15 (0.20), residues: 643 sheet: -0.73 (0.14), residues: 1281 loop : -1.89 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 319 TYR 0.018 0.002 TYR B1067 PHE 0.022 0.002 PHE A 906 TRP 0.015 0.002 TRP B 104 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00505 (34272) covalent geometry : angle 0.63645 (46669) SS BOND : bond 0.00451 ( 48) SS BOND : angle 1.40689 ( 96) hydrogen bonds : bond 0.05038 ( 1286) hydrogen bonds : angle 5.80784 ( 3411) link_NAG-ASN : bond 0.00586 ( 27) link_NAG-ASN : angle 3.40023 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 1.260 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: B 346 ARG cc_start: 0.5026 (OUTLIER) cc_final: 0.4769 (ppt-90) REVERT: B 697 MET cc_start: 0.8955 (ptp) cc_final: 0.7966 (pmm) REVERT: A 1050 MET cc_start: 0.7533 (mtp) cc_final: 0.7154 (mtp) REVERT: C 1072 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: X 95 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8032 (pp30) REVERT: Y 34 MET cc_start: 0.7085 (mpp) cc_final: 0.6864 (mpp) REVERT: H 34 MET cc_start: 0.1508 (mmm) cc_final: 0.0959 (mmm) outliers start: 36 outliers final: 14 residues processed: 138 average time/residue: 0.2206 time to fit residues: 49.9744 Evaluate side-chains 103 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain X residue 54 TYR Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 73 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 346 optimal weight: 30.0000 chunk 262 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 804 GLN A 935 GLN A1010 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 163 ASN P 3 GLN X 95 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.086005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.057014 restraints weight = 213243.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.052916 restraints weight = 95738.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.052881 restraints weight = 59464.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.053161 restraints weight = 43978.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.053308 restraints weight = 36347.748| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34347 Z= 0.133 Angle : 0.570 13.537 46846 Z= 0.290 Chirality : 0.044 0.336 5400 Planarity : 0.004 0.060 6011 Dihedral : 7.416 117.396 5156 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.52 % Allowed : 12.65 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.23 (0.13), residues: 4233 helix: 1.54 (0.21), residues: 650 sheet: -0.55 (0.14), residues: 1293 loop : -1.72 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 24 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE X 76 TRP 0.014 0.001 TRP B 104 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00301 (34272) covalent geometry : angle 0.55279 (46669) SS BOND : bond 0.00300 ( 48) SS BOND : angle 1.23884 ( 96) hydrogen bonds : bond 0.04254 ( 1286) hydrogen bonds : angle 5.39280 ( 3411) link_NAG-ASN : bond 0.00478 ( 27) link_NAG-ASN : angle 3.18329 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 93 time to evaluate : 1.298 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: B 697 MET cc_start: 0.8964 (ptp) cc_final: 0.7977 (pmm) REVERT: A 303 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8592 (tt) REVERT: A 671 CYS cc_start: 0.6469 (OUTLIER) cc_final: 0.5820 (p) REVERT: X 94 MET cc_start: 0.7746 (tpp) cc_final: 0.7291 (tpp) REVERT: X 95 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7696 (pp30) REVERT: Y 73 ASP cc_start: 0.9236 (t0) cc_final: 0.8526 (p0) REVERT: Y 83 MET cc_start: 0.8784 (mtm) cc_final: 0.8443 (mpp) REVERT: Y 160 LYS cc_start: 0.8784 (pttm) cc_final: 0.8219 (tptp) outliers start: 56 outliers final: 22 residues processed: 144 average time/residue: 0.1913 time to fit residues: 46.7596 Evaluate side-chains 111 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain X residue 54 TYR Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain Y residue 134 LYS Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 301 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 83 optimal weight: 0.2980 chunk 221 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 342 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 overall best weight: 5.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 953 ASN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN X 95 GLN Y 181 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.084458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055113 restraints weight = 213923.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.050799 restraints weight = 96746.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.050607 restraints weight = 62813.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.050807 restraints weight = 47002.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.050927 restraints weight = 40295.241| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 34347 Z= 0.246 Angle : 0.658 14.498 46846 Z= 0.336 Chirality : 0.046 0.410 5400 Planarity : 0.005 0.065 6011 Dihedral : 7.815 120.229 5156 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.98 % Allowed : 13.59 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.38 (0.13), residues: 4233 helix: 1.18 (0.20), residues: 644 sheet: -0.59 (0.14), residues: 1302 loop : -1.77 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 24 TYR 0.018 0.002 TYR B1067 PHE 0.019 0.002 PHE A 855 TRP 0.013 0.002 TRP P 171 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00563 (34272) covalent geometry : angle 0.64148 (46669) SS BOND : bond 0.00545 ( 48) SS BOND : angle 1.44573 ( 96) hydrogen bonds : bond 0.05144 ( 1286) hydrogen bonds : angle 5.72353 ( 3411) link_NAG-ASN : bond 0.00508 ( 27) link_NAG-ASN : angle 3.25017 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 89 time to evaluate : 1.311 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: B 697 MET cc_start: 0.8981 (ptp) cc_final: 0.8580 (pmm) REVERT: B 759 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8305 (m-80) REVERT: B 878 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8468 (mp) REVERT: A 303 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8543 (tt) REVERT: A 671 CYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6501 (p) REVERT: X 94 MET cc_start: 0.7843 (tpp) cc_final: 0.7139 (mmm) REVERT: X 95 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8031 (pp30) REVERT: X 170 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9280 (pm20) REVERT: X 174 LYS cc_start: 0.7106 (pttt) cc_final: 0.6519 (pttm) REVERT: Y 83 MET cc_start: 0.8713 (mtm) cc_final: 0.8335 (mpp) outliers start: 73 outliers final: 41 residues processed: 159 average time/residue: 0.1929 time to fit residues: 52.4108 Evaluate side-chains 127 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 134 LYS Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 124 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 370 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 330 optimal weight: 50.0000 chunk 9 optimal weight: 3.9990 chunk 399 optimal weight: 30.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 163 ASN P 3 GLN X 95 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.085218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.056046 restraints weight = 213638.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.052694 restraints weight = 95627.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.052895 restraints weight = 60829.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053162 restraints weight = 45702.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.053361 restraints weight = 36954.213| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34347 Z= 0.144 Angle : 0.574 13.630 46846 Z= 0.292 Chirality : 0.044 0.336 5400 Planarity : 0.004 0.069 6011 Dihedral : 7.373 118.226 5156 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.79 % Allowed : 14.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.14 (0.13), residues: 4233 helix: 1.56 (0.21), residues: 644 sheet: -0.49 (0.14), residues: 1325 loop : -1.65 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 216 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE A 888 TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00328 (34272) covalent geometry : angle 0.55770 (46669) SS BOND : bond 0.00371 ( 48) SS BOND : angle 1.24479 ( 96) hydrogen bonds : bond 0.04299 ( 1286) hydrogen bonds : angle 5.31486 ( 3411) link_NAG-ASN : bond 0.00448 ( 27) link_NAG-ASN : angle 3.06795 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 88 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8939 (ptp) cc_final: 0.8068 (pmm) REVERT: B 902 MET cc_start: 0.9217 (tpp) cc_final: 0.8913 (tpp) REVERT: A 303 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8570 (tt) REVERT: A 671 CYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6318 (p) REVERT: X 94 MET cc_start: 0.8478 (tpp) cc_final: 0.7638 (mmm) REVERT: X 95 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.7704 (pp30) REVERT: X 170 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9274 (pm20) REVERT: X 174 LYS cc_start: 0.7111 (pttt) cc_final: 0.6494 (pttm) REVERT: Y 83 MET cc_start: 0.8698 (mtm) cc_final: 0.8204 (mpp) outliers start: 66 outliers final: 38 residues processed: 150 average time/residue: 0.1941 time to fit residues: 50.1443 Evaluate side-chains 121 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain X residue 54 TYR Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 404 optimal weight: 6.9990 chunk 341 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 301 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 418 optimal weight: 9.9990 chunk 390 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 GLN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 95 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.084972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.055770 restraints weight = 215037.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.051758 restraints weight = 96080.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.051848 restraints weight = 62050.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.051982 restraints weight = 45544.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.052229 restraints weight = 37619.812| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34347 Z= 0.167 Angle : 0.584 13.851 46846 Z= 0.297 Chirality : 0.045 0.352 5400 Planarity : 0.004 0.071 6011 Dihedral : 7.372 118.876 5156 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.95 % Allowed : 14.92 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.09 (0.13), residues: 4233 helix: 1.51 (0.21), residues: 650 sheet: -0.48 (0.14), residues: 1330 loop : -1.58 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE A 888 TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS O 194 Details of bonding type rmsd covalent geometry : bond 0.00385 (34272) covalent geometry : angle 0.56837 (46669) SS BOND : bond 0.00358 ( 48) SS BOND : angle 1.18050 ( 96) hydrogen bonds : bond 0.04393 ( 1286) hydrogen bonds : angle 5.31986 ( 3411) link_NAG-ASN : bond 0.00461 ( 27) link_NAG-ASN : angle 3.04989 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 84 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8930 (ptp) cc_final: 0.8023 (pmm) REVERT: A 303 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8597 (tt) REVERT: A 671 CYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6320 (p) REVERT: X 94 MET cc_start: 0.8567 (tpp) cc_final: 0.7833 (mmm) REVERT: X 95 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.7972 (pp30) REVERT: X 170 GLU cc_start: 0.9614 (mm-30) cc_final: 0.9235 (pm20) REVERT: Y 83 MET cc_start: 0.8715 (mtm) cc_final: 0.8205 (mpp) REVERT: H 117 MET cc_start: 0.3353 (tpt) cc_final: 0.2456 (tpp) outliers start: 72 outliers final: 49 residues processed: 154 average time/residue: 0.1804 time to fit residues: 47.9673 Evaluate side-chains 132 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 80 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain X residue 54 TYR Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 90 optimal weight: 1.9990 chunk 409 optimal weight: 20.0000 chunk 69 optimal weight: 0.0010 chunk 189 optimal weight: 2.9990 chunk 214 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 342 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 246 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 GLN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 95 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.084780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.055613 restraints weight = 214339.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051807 restraints weight = 95699.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.051942 restraints weight = 59986.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.052279 restraints weight = 45907.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.052355 restraints weight = 37943.357| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34347 Z= 0.176 Angle : 0.592 13.874 46846 Z= 0.301 Chirality : 0.045 0.351 5400 Planarity : 0.004 0.071 6011 Dihedral : 7.377 118.879 5156 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.92 % Allowed : 15.19 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.07 (0.13), residues: 4233 helix: 1.49 (0.21), residues: 650 sheet: -0.43 (0.14), residues: 1342 loop : -1.60 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE B1121 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00404 (34272) covalent geometry : angle 0.57635 (46669) SS BOND : bond 0.00358 ( 48) SS BOND : angle 1.22789 ( 96) hydrogen bonds : bond 0.04418 ( 1286) hydrogen bonds : angle 5.33794 ( 3411) link_NAG-ASN : bond 0.00443 ( 27) link_NAG-ASN : angle 3.04246 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 82 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 ARG cc_start: 0.4112 (OUTLIER) cc_final: 0.3878 (ppt-90) REVERT: B 697 MET cc_start: 0.8930 (ptp) cc_final: 0.8557 (pmm) REVERT: A 200 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8552 (m-10) REVERT: A 204 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: C 398 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.7742 (t0) REVERT: O 94 MET cc_start: 0.7677 (tpt) cc_final: 0.6992 (tmm) REVERT: P 117 MET cc_start: 0.7645 (mmm) cc_final: 0.7098 (mmm) REVERT: X 94 MET cc_start: 0.8656 (tpp) cc_final: 0.7993 (mmm) REVERT: X 95 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8316 (pp30) REVERT: X 170 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9235 (pm20) REVERT: Y 76 LYS cc_start: 0.8962 (ptpp) cc_final: 0.8250 (mmtt) REVERT: Y 83 MET cc_start: 0.8790 (mtm) cc_final: 0.8242 (mpp) REVERT: H 34 MET cc_start: -0.0367 (mmm) cc_final: -0.0745 (mtp) REVERT: H 117 MET cc_start: 0.3509 (OUTLIER) cc_final: 0.2151 (tpp) outliers start: 71 outliers final: 56 residues processed: 149 average time/residue: 0.1868 time to fit residues: 47.7718 Evaluate side-chains 142 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 80 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain X residue 54 TYR Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 249 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 352 optimal weight: 40.0000 chunk 287 optimal weight: 0.9980 chunk 365 optimal weight: 7.9990 chunk 204 optimal weight: 0.0070 chunk 410 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 360 optimal weight: 0.0570 chunk 339 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN A 49 HIS A 965 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 214 ASN ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.086077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.057323 restraints weight = 213383.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.052418 restraints weight = 95424.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.051781 restraints weight = 61290.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.052049 restraints weight = 45594.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.052133 restraints weight = 38251.865| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34347 Z= 0.099 Angle : 0.541 12.831 46846 Z= 0.272 Chirality : 0.044 0.285 5400 Planarity : 0.004 0.072 6011 Dihedral : 6.877 115.786 5156 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.27 % Allowed : 15.84 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.82 (0.13), residues: 4233 helix: 1.92 (0.21), residues: 645 sheet: -0.30 (0.14), residues: 1361 loop : -1.48 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 102 TYR 0.014 0.001 TYR B1067 PHE 0.015 0.001 PHE A 888 TRP 0.014 0.001 TRP B 104 HIS 0.004 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00215 (34272) covalent geometry : angle 0.52678 (46669) SS BOND : bond 0.00232 ( 48) SS BOND : angle 0.96808 ( 96) hydrogen bonds : bond 0.03634 ( 1286) hydrogen bonds : angle 4.93844 ( 3411) link_NAG-ASN : bond 0.00460 ( 27) link_NAG-ASN : angle 2.86444 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 89 time to evaluate : 1.134 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: B 346 ARG cc_start: 0.3870 (OUTLIER) cc_final: 0.3617 (ppt-90) REVERT: B 697 MET cc_start: 0.8748 (ptp) cc_final: 0.7908 (pmm) REVERT: A 200 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8521 (m-10) REVERT: A 1068 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8864 (m) REVERT: P 117 MET cc_start: 0.7651 (mmm) cc_final: 0.7358 (mmm) REVERT: X 170 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9197 (pm20) REVERT: Y 76 LYS cc_start: 0.8851 (ptpp) cc_final: 0.8160 (mmtt) REVERT: Y 83 MET cc_start: 0.8770 (mtm) cc_final: 0.8461 (mpp) REVERT: H 34 MET cc_start: 0.0846 (mmm) cc_final: 0.0443 (mtp) REVERT: H 117 MET cc_start: 0.3252 (OUTLIER) cc_final: 0.2250 (tpp) outliers start: 47 outliers final: 38 residues processed: 130 average time/residue: 0.1983 time to fit residues: 43.5684 Evaluate side-chains 123 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain X residue 54 TYR Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 152 GLN Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 7 optimal weight: 7.9990 chunk 381 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 420 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 349 optimal weight: 8.9990 chunk 168 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 chunk 416 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.4062 r_free = 0.4062 target = 0.085100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.055912 restraints weight = 214597.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.051920 restraints weight = 95561.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.052330 restraints weight = 60927.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.052651 restraints weight = 44809.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.052691 restraints weight = 36226.849| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34347 Z= 0.152 Angle : 0.575 13.611 46846 Z= 0.289 Chirality : 0.044 0.339 5400 Planarity : 0.004 0.071 6011 Dihedral : 7.053 117.749 5156 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.41 % Allowed : 15.89 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.83 (0.13), residues: 4233 helix: 1.79 (0.21), residues: 651 sheet: -0.31 (0.14), residues: 1364 loop : -1.45 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 24 TYR 0.015 0.001 TYR B1067 PHE 0.015 0.001 PHE C 456 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00351 (34272) covalent geometry : angle 0.56059 (46669) SS BOND : bond 0.00330 ( 48) SS BOND : angle 1.08992 ( 96) hydrogen bonds : bond 0.04073 ( 1286) hydrogen bonds : angle 5.10313 ( 3411) link_NAG-ASN : bond 0.00439 ( 27) link_NAG-ASN : angle 2.92640 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 75 time to evaluate : 1.225 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: B 346 ARG cc_start: 0.4060 (OUTLIER) cc_final: 0.3837 (ppt-90) REVERT: B 697 MET cc_start: 0.8833 (ptp) cc_final: 0.7969 (pmm) REVERT: A 200 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8450 (m-10) REVERT: A 204 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7624 (m-10) REVERT: P 117 MET cc_start: 0.7809 (mmm) cc_final: 0.7546 (mmm) REVERT: X 170 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9218 (pm20) REVERT: Y 83 MET cc_start: 0.8722 (mtm) cc_final: 0.8184 (mpp) REVERT: H 34 MET cc_start: -0.0064 (mmm) cc_final: -0.0437 (mtp) REVERT: H 117 MET cc_start: 0.3318 (OUTLIER) cc_final: 0.2350 (tpp) outliers start: 52 outliers final: 44 residues processed: 122 average time/residue: 0.2078 time to fit residues: 42.7206 Evaluate side-chains 121 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 73 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain X residue 54 TYR Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 152 GLN Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 401 optimal weight: 50.0000 chunk 104 optimal weight: 0.0870 chunk 264 optimal weight: 0.5980 chunk 326 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 280 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 95 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.085376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.056387 restraints weight = 213555.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.053101 restraints weight = 96542.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.053524 restraints weight = 57716.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.053714 restraints weight = 42628.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.053557 restraints weight = 35729.681| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34347 Z= 0.126 Angle : 0.557 13.288 46846 Z= 0.280 Chirality : 0.044 0.323 5400 Planarity : 0.004 0.071 6011 Dihedral : 6.967 117.116 5156 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.52 % Allowed : 15.95 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.74 (0.13), residues: 4233 helix: 1.91 (0.21), residues: 645 sheet: -0.25 (0.14), residues: 1366 loop : -1.41 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 24 TYR 0.015 0.001 TYR O 41 PHE 0.015 0.001 PHE C 456 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00289 (34272) covalent geometry : angle 0.54327 (46669) SS BOND : bond 0.00296 ( 48) SS BOND : angle 1.02342 ( 96) hydrogen bonds : bond 0.03902 ( 1286) hydrogen bonds : angle 5.01932 ( 3411) link_NAG-ASN : bond 0.00440 ( 27) link_NAG-ASN : angle 2.88158 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9212.59 seconds wall clock time: 158 minutes 5.87 seconds (9485.87 seconds total)