Starting phenix.real_space_refine on Fri Mar 6 00:20:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6g_23695/03_2026/7m6g_23695_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6g_23695/03_2026/7m6g_23695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6g_23695/03_2026/7m6g_23695_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6g_23695/03_2026/7m6g_23695_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6g_23695/03_2026/7m6g_23695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6g_23695/03_2026/7m6g_23695.map" } resolution = 3.7 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= 0.018 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 117 5.16 5 C 16719 2.51 5 N 4316 2.21 5 O 5138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s 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: 26290 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7393 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 8, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7427 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 53, 'TRANS': 927} Chain breaks: 10 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 6, 'ARG:plan': 6, 'GLN:plan1': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'TYR:plan': 4, 'ASP:plan': 8, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 177 Chain: "C" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7408 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 53, 'TRANS': 931} Chain breaks: 10 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 6, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 208 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "R" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "S" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.97, per 1000 atoms: 0.23 Number of scatterers: 26290 At special positions: 0 Unit cell: (137.302, 135.564, 198.132, 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 117 16.00 O 5138 8.00 N 4316 7.00 C 16719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 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=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 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=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 616 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 616 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN C 801 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN C1074 " " NAG O 1 " - " ASN A1074 " " NAG P 1 " - " ASN C 717 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6316 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 54 sheets defined 23.7% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.649A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.087A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.582A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.700A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.265A 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 982 removed outlier: 3.628A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.887A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.029A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.970A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.535A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 4.197A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.704A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.752A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.924A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.956A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.769A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.812A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.394A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.924A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.463A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 140 through 140 No H-bonds generated for 'chain 'C' and resid 140 through 140' Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.938A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.584A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.839A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.544A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.930A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.725A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.671A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.033A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 984 removed outlier: 3.923A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.446A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.406A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.505A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 83 through 87 removed outlier: 3.513A pdb=" N THR R 87 " --> pdb=" O SER R 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.058A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 79 through 83 removed outlier: 3.675A pdb=" N PHE S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.741A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.634A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.804A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.163A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.728A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 543 removed outlier: 4.763A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.681A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.600A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.312A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.577A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.462A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.772A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.781A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.074A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.537A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.585A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.739A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.875A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.875A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.185A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.004A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.004A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.823A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.599A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.811A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.655A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.688A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.507A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.608A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.780A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.535A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.312A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.866A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.650A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 3 through 6 removed outlier: 3.769A pdb=" N CYS R 22 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA R 78 " --> pdb=" O CYS R 22 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU R 81 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR R 68 " --> pdb=" O GLU R 81 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.258A pdb=" N GLU R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR R 107 " --> pdb=" O TYR R 90 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP R 50 " --> pdb=" O ASN R 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN R 58 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.240A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 19 through 28 removed outlier: 12.024A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.809A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.522A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY L 68 " --> pdb=" O VAL L 28 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.547A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.738A pdb=" N LEU S 11 " --> pdb=" O GLU S 105 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR S 102 " --> pdb=" O TYR S 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR S 86 " --> pdb=" O THR S 102 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL S 85 " --> pdb=" O GLN S 38 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU S 33 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN S 37 " --> pdb=" O ARG S 45 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER S 53 " --> pdb=" O SER S 49 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 19 through 24 removed outlier: 3.829A pdb=" N ALA S 19 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE S 75 " --> pdb=" O ALA S 19 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU S 21 " --> pdb=" O LEU S 73 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU S 73 " --> pdb=" O LEU S 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE S 71 " --> pdb=" O CYS S 23 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2658 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: 6.01 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8214 1.34 - 1.48: 7251 1.48 - 1.62: 11242 1.62 - 1.76: 8 1.76 - 1.90: 139 Bond restraints: 26854 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CG PRO C 507 " pdb=" CD PRO C 507 " ideal model delta sigma weight residual 1.503 1.339 0.164 3.40e-02 8.65e+02 2.34e+01 ... (remaining 26849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.11: 36294 6.11 - 12.21: 292 12.21 - 18.32: 23 18.32 - 24.42: 1 24.42 - 30.53: 1 Bond angle restraints: 36611 Sorted by residual: angle pdb=" CA LEU B 948 " pdb=" CB LEU B 948 " pdb=" CG LEU B 948 " ideal model delta sigma weight residual 116.30 146.83 -30.53 3.50e+00 8.16e-02 7.61e+01 angle pdb=" N PRO C 507 " pdb=" CD PRO C 507 " pdb=" CG PRO C 507 " ideal model delta sigma weight residual 103.20 90.38 12.82 1.50e+00 4.44e-01 7.31e+01 angle pdb=" CA PRO A1079 " pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 112.00 100.43 11.57 1.40e+00 5.10e-01 6.84e+01 angle pdb=" CA PRO C1079 " pdb=" N PRO C1079 " pdb=" CD PRO C1079 " ideal model delta sigma weight residual 112.00 100.57 11.43 1.40e+00 5.10e-01 6.67e+01 angle pdb=" N ASN A1098 " pdb=" CA ASN A1098 " pdb=" CB ASN A1098 " ideal model delta sigma weight residual 110.44 98.36 12.08 1.53e+00 4.27e-01 6.24e+01 ... (remaining 36606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 15707 24.43 - 48.86: 714 48.86 - 73.29: 113 73.29 - 97.71: 35 97.71 - 122.14: 14 Dihedral angle restraints: 16583 sinusoidal: 6785 harmonic: 9798 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 3.74 89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.20 -77.80 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -161.78 75.78 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 16580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 4328 0.304 - 0.608: 45 0.608 - 0.912: 2 0.912 - 1.216: 2 1.216 - 1.520: 1 Chirality restraints: 4378 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.88 -1.52 2.00e-01 2.50e+01 5.77e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.25 -1.15 2.00e-01 2.50e+01 3.28e+01 ... (remaining 4375 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " 0.320 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG B1311 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.320 2.00e-02 2.50e+03 2.74e-01 9.40e+02 pdb=" C7 NAG D 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.170 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.265 2.00e-02 2.50e+03 2.25e-01 6.35e+02 pdb=" C7 NAG A1307 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.388 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.019 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2292 2.75 - 3.28: 25088 3.28 - 3.82: 41332 3.82 - 4.36: 47791 4.36 - 4.90: 81941 Nonbonded interactions: 198444 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.208 3.040 nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.220 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.223 3.040 nonbonded pdb=" O PHE B 106 " pdb=" OG SER B 116 " model vdw 2.228 3.040 ... (remaining 198439 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 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 243 or resid 264 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 350 or (resid 351 through 352 and (name N or name CA or na \ me C or name O or name CB )) or resid 353 through 363 or (resid 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 368 or (resid \ 369 and (name N or name CA or name C or name O or name CB )) or resid 370 throug \ h 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) or \ resid 375 through 407 or (resid 408 and (name N or name CA or name C or name O o \ r name CB )) or resid 409 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 or (resid 449 and (name N or name CA o \ r name C or name O or name CB )) or resid 450 through 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 or (re \ sid 500 and (name N or name CA or name C or name O or name CB )) or resid 503 th \ rough 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 620 or resid 641 through 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 443 or resid 449 through 454 or resid 491 th \ rough 500 or resid 503 through 528 or (resid 529 and (name N or name CA or name \ C or name O or name CB )) or resid 530 through 620 or resid 641 through 1307)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 443 or re \ sid 449 through 454 or resid 491 through 500 or resid 503 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'R' } ncs_group { reference = chain 'L' selection = chain 'S' } 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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.370 Find NCS groups from input model: 0.830 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 0.164 26941 Z= 0.425 Angle : 1.642 30.530 36832 Z= 0.888 Chirality : 0.096 1.520 4378 Planarity : 0.014 0.279 4666 Dihedral : 14.408 122.143 10147 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 0.47 % Allowed : 1.30 % Favored : 98.23 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 3304 helix: -0.17 (0.18), residues: 672 sheet: 0.96 (0.18), residues: 716 loop : -0.86 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.004 ARG B 995 TYR 0.064 0.004 TYR H 59 PHE 0.104 0.005 PHE C 392 TRP 0.055 0.004 TRP C 104 HIS 0.037 0.004 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00857 (26854) covalent geometry : angle 1.55052 (36611) SS BOND : bond 0.01302 ( 40) SS BOND : angle 3.98403 ( 80) hydrogen bonds : bond 0.23067 ( 949) hydrogen bonds : angle 8.92306 ( 2658) link_BETA1-4 : bond 0.00854 ( 11) link_BETA1-4 : angle 3.18929 ( 33) link_NAG-ASN : bond 0.01739 ( 36) link_NAG-ASN : angle 9.48827 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 501 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7979 (m-80) cc_final: 0.7651 (m-10) REVERT: A 106 PHE cc_start: 0.8739 (m-80) cc_final: 0.8515 (m-80) REVERT: A 223 LEU cc_start: 0.7977 (mm) cc_final: 0.7638 (mt) REVERT: A 298 GLU cc_start: 0.8366 (tp30) cc_final: 0.7953 (mt-10) REVERT: A 611 LEU cc_start: 0.8417 (tp) cc_final: 0.8146 (tt) REVERT: A 671 CYS cc_start: 0.3818 (m) cc_final: 0.2506 (m) REVERT: A 737 ASP cc_start: 0.7528 (p0) cc_final: 0.7110 (p0) REVERT: A 974 SER cc_start: 0.7624 (t) cc_final: 0.7369 (t) REVERT: B 200 TYR cc_start: 0.6556 (m-80) cc_final: 0.6341 (m-10) REVERT: B 290 ASP cc_start: 0.7053 (p0) cc_final: 0.6823 (p0) REVERT: B 731 MET cc_start: 0.7696 (ptm) cc_final: 0.7336 (ptm) REVERT: B 855 PHE cc_start: 0.5247 (m-80) cc_final: 0.5000 (m-80) REVERT: C 443 SER cc_start: 0.8556 (m) cc_final: 0.7681 (m) REVERT: C 918 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: H 59 TYR cc_start: 0.6350 (m-80) cc_final: 0.6021 (m-80) REVERT: H 64 GLN cc_start: 0.8284 (tp40) cc_final: 0.7809 (mm-40) REVERT: H 69 MET cc_start: 0.8175 (mpp) cc_final: 0.7800 (mpp) REVERT: H 99 VAL cc_start: 0.7244 (t) cc_final: 0.7019 (p) REVERT: H 101 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6680 (t70) REVERT: H 102 CYS cc_start: 0.7108 (m) cc_final: 0.6811 (m) REVERT: R 50 TRP cc_start: 0.6014 (p-90) cc_final: 0.5012 (p-90) REVERT: R 91 TYR cc_start: 0.5945 (m-80) cc_final: 0.5723 (m-80) REVERT: R 101 ASP cc_start: 0.8407 (m-30) cc_final: 0.7790 (m-30) REVERT: R 105 GLN cc_start: 0.4053 (OUTLIER) cc_final: 0.3754 (pm20) REVERT: L 33 LEU cc_start: 0.8680 (mt) cc_final: 0.8452 (mt) REVERT: L 39 LYS cc_start: 0.7448 (tptt) cc_final: 0.7103 (mmtm) REVERT: L 89 GLN cc_start: 0.6631 (tm-30) cc_final: 0.4735 (tp-100) REVERT: L 91 TYR cc_start: 0.7687 (p90) cc_final: 0.7155 (p90) REVERT: S 47 LEU cc_start: 0.8916 (mp) cc_final: 0.8095 (pp) REVERT: S 103 LYS cc_start: 0.4556 (tptp) cc_final: 0.4345 (mmmt) outliers start: 13 outliers final: 2 residues processed: 511 average time/residue: 0.1465 time to fit residues: 124.7482 Evaluate side-chains 334 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 329 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain R residue 105 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN A1005 GLN B 134 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1083 HIS C1088 HIS S 6 GLN ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.132980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.102805 restraints weight = 75287.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.105963 restraints weight = 43756.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.107888 restraints weight = 23084.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.107995 restraints weight = 18153.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.108212 restraints weight = 16481.602| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26941 Z= 0.238 Angle : 0.894 21.651 36832 Z= 0.437 Chirality : 0.054 0.648 4378 Planarity : 0.006 0.094 4666 Dihedral : 10.071 115.162 4598 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 2.35 % Allowed : 10.59 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3304 helix: 0.07 (0.19), residues: 680 sheet: 0.61 (0.18), residues: 773 loop : -0.65 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 319 TYR 0.024 0.002 TYR B 917 PHE 0.037 0.003 PHE L 83 TRP 0.026 0.003 TRP H 103 HIS 0.008 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00531 (26854) covalent geometry : angle 0.81642 (36611) SS BOND : bond 0.00525 ( 40) SS BOND : angle 2.13342 ( 80) hydrogen bonds : bond 0.05245 ( 949) hydrogen bonds : angle 6.94163 ( 2658) link_BETA1-4 : bond 0.00904 ( 11) link_BETA1-4 : angle 2.25955 ( 33) link_NAG-ASN : bond 0.00875 ( 36) link_NAG-ASN : angle 6.43841 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 337 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8196 (t80) REVERT: A 819 GLU cc_start: 0.7175 (pt0) cc_final: 0.6894 (tt0) REVERT: A 974 SER cc_start: 0.8280 (t) cc_final: 0.8002 (t) REVERT: B 200 TYR cc_start: 0.6786 (m-10) cc_final: 0.6133 (m-10) REVERT: B 338 PHE cc_start: 0.6839 (m-80) cc_final: 0.6588 (m-10) REVERT: B 409 GLN cc_start: 0.8420 (mt0) cc_final: 0.8158 (mt0) REVERT: B 712 ILE cc_start: 0.5622 (OUTLIER) cc_final: 0.5394 (mm) REVERT: C 43 PHE cc_start: 0.7084 (t80) cc_final: 0.6721 (t80) REVERT: C 315 THR cc_start: 0.8244 (p) cc_final: 0.8027 (t) REVERT: C 574 ASP cc_start: 0.6497 (m-30) cc_final: 0.6280 (m-30) REVERT: C 712 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6605 (mm) REVERT: C 918 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: R 101 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: R 105 GLN cc_start: 0.4065 (OUTLIER) cc_final: 0.3799 (pm20) REVERT: L 39 LYS cc_start: 0.7898 (tptt) cc_final: 0.7541 (mptt) REVERT: L 71 PHE cc_start: 0.7062 (m-80) cc_final: 0.6826 (m-10) REVERT: S 54 ARG cc_start: 0.6148 (ptp90) cc_final: 0.5454 (ptp-170) REVERT: S 103 LYS cc_start: 0.4520 (tptp) cc_final: 0.4317 (mmmt) outliers start: 65 outliers final: 38 residues processed: 383 average time/residue: 0.1481 time to fit residues: 95.3440 Evaluate side-chains 313 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 105 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 230 optimal weight: 4.9990 chunk 267 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 299 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 895 GLN A 955 ASN B 755 GLN B 955 ASN B 965 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.133199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.103182 restraints weight = 75220.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.106211 restraints weight = 45486.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107138 restraints weight = 25826.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.107992 restraints weight = 20037.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.108219 restraints weight = 17390.664| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26941 Z= 0.152 Angle : 0.770 21.516 36832 Z= 0.371 Chirality : 0.050 0.513 4378 Planarity : 0.005 0.069 4666 Dihedral : 9.012 113.205 4596 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.96 % Allowed : 13.16 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3304 helix: 0.00 (0.19), residues: 683 sheet: 0.53 (0.17), residues: 784 loop : -0.58 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 95 TYR 0.023 0.002 TYR B 38 PHE 0.030 0.002 PHE C 86 TRP 0.048 0.002 TRP H 103 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00340 (26854) covalent geometry : angle 0.69674 (36611) SS BOND : bond 0.00471 ( 40) SS BOND : angle 1.88463 ( 80) hydrogen bonds : bond 0.04364 ( 949) hydrogen bonds : angle 6.39679 ( 2658) link_BETA1-4 : bond 0.00569 ( 11) link_BETA1-4 : angle 2.18847 ( 33) link_NAG-ASN : bond 0.00818 ( 36) link_NAG-ASN : angle 5.77240 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 305 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (mmm) REVERT: A 902 MET cc_start: 0.8510 (tpt) cc_final: 0.7997 (tpt) REVERT: A 974 SER cc_start: 0.8450 (t) cc_final: 0.8190 (t) REVERT: B 49 HIS cc_start: 0.7015 (t-170) cc_final: 0.6789 (t-170) REVERT: B 129 LYS cc_start: 0.6869 (tptm) cc_final: 0.6631 (tptm) REVERT: B 200 TYR cc_start: 0.6759 (m-80) cc_final: 0.6018 (m-10) REVERT: B 298 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: B 983 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7091 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8370 (tp40) cc_final: 0.8133 (tp40) REVERT: B 1050 MET cc_start: 0.7191 (ptm) cc_final: 0.6913 (ptm) REVERT: C 223 LEU cc_start: 0.6586 (tp) cc_final: 0.6385 (tp) REVERT: C 265 TYR cc_start: 0.5510 (p90) cc_final: 0.5014 (p90) REVERT: C 315 THR cc_start: 0.8317 (p) cc_final: 0.8104 (t) REVERT: C 918 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: C 1050 MET cc_start: 0.6888 (ptm) cc_final: 0.6158 (ptt) REVERT: H 59 TYR cc_start: 0.6623 (m-80) cc_final: 0.5900 (m-80) REVERT: H 64 GLN cc_start: 0.8186 (tp40) cc_final: 0.7834 (mm-40) REVERT: H 69 MET cc_start: 0.8154 (mpp) cc_final: 0.7852 (mpp) REVERT: H 103 TRP cc_start: 0.6962 (m100) cc_final: 0.6197 (m100) REVERT: R 80 MET cc_start: 0.3497 (mmp) cc_final: 0.2856 (mmp) REVERT: R 101 ASP cc_start: 0.8199 (m-30) cc_final: 0.7397 (m-30) REVERT: L 39 LYS cc_start: 0.7912 (tptt) cc_final: 0.7537 (mptt) REVERT: S 54 ARG cc_start: 0.6033 (ptp90) cc_final: 0.5319 (ptp-170) REVERT: S 79 GLU cc_start: 0.7851 (tp30) cc_final: 0.7605 (tp30) outliers start: 82 outliers final: 52 residues processed: 367 average time/residue: 0.1435 time to fit residues: 88.1229 Evaluate side-chains 323 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 267 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 GLU Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 76 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 328 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 305 optimal weight: 20.0000 chunk 262 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 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 = 0.4110 r_free = 0.4110 target = 0.131266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100174 restraints weight = 73122.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.103258 restraints weight = 41626.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104396 restraints weight = 23645.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105212 restraints weight = 17750.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105239 restraints weight = 15925.666| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 26941 Z= 0.192 Angle : 0.756 20.911 36832 Z= 0.368 Chirality : 0.049 0.462 4378 Planarity : 0.005 0.059 4666 Dihedral : 8.418 110.971 4591 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.23 % Allowed : 13.88 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3304 helix: -0.05 (0.19), residues: 681 sheet: 0.51 (0.17), residues: 777 loop : -0.64 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1107 TYR 0.018 0.002 TYR A 741 PHE 0.021 0.002 PHE L 71 TRP 0.027 0.002 TRP H 103 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00441 (26854) covalent geometry : angle 0.68887 (36611) SS BOND : bond 0.00449 ( 40) SS BOND : angle 1.79045 ( 80) hydrogen bonds : bond 0.04227 ( 949) hydrogen bonds : angle 6.20270 ( 2658) link_BETA1-4 : bond 0.00563 ( 11) link_BETA1-4 : angle 1.96464 ( 33) link_NAG-ASN : bond 0.00816 ( 36) link_NAG-ASN : angle 5.52837 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 298 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8248 (mm110) REVERT: A 220 PHE cc_start: 0.7798 (t80) cc_final: 0.7334 (t80) REVERT: A 737 ASP cc_start: 0.7716 (p0) cc_final: 0.7112 (p0) REVERT: A 740 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7300 (mpp) REVERT: A 759 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7983 (t80) REVERT: A 894 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8278 (pp) REVERT: A 974 SER cc_start: 0.8808 (t) cc_final: 0.8574 (t) REVERT: B 129 LYS cc_start: 0.6857 (tptm) cc_final: 0.6582 (tptm) REVERT: B 204 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.5795 (m-80) REVERT: B 584 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7439 (pt) REVERT: B 983 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7372 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8452 (tp40) cc_final: 0.7999 (tp40) REVERT: C 223 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6550 (tp) REVERT: C 235 ILE cc_start: 0.3947 (OUTLIER) cc_final: 0.3735 (mt) REVERT: C 265 TYR cc_start: 0.6174 (p90) cc_final: 0.5704 (p90) REVERT: C 574 ASP cc_start: 0.6510 (m-30) cc_final: 0.6170 (m-30) REVERT: C 918 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: C 1050 MET cc_start: 0.6998 (ptm) cc_final: 0.6405 (ptt) REVERT: H 59 TYR cc_start: 0.6666 (m-80) cc_final: 0.5838 (m-80) REVERT: H 64 GLN cc_start: 0.8197 (tp40) cc_final: 0.7794 (mm-40) REVERT: R 96 TYR cc_start: 0.7818 (t80) cc_final: 0.7538 (t80) REVERT: R 101 ASP cc_start: 0.7995 (m-30) cc_final: 0.7355 (m-30) REVERT: L 35 TRP cc_start: 0.6777 (m-10) cc_final: 0.6567 (m-10) REVERT: L 39 LYS cc_start: 0.7900 (tptt) cc_final: 0.7466 (mptt) REVERT: S 54 ARG cc_start: 0.6020 (ptp90) cc_final: 0.5333 (ptp-170) outliers start: 117 outliers final: 77 residues processed: 387 average time/residue: 0.1337 time to fit residues: 88.1490 Evaluate side-chains 349 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 262 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 174 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 312 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 655 HIS A 895 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 409 GLN B 913 GLN B1005 GLN B1010 GLN C 218 GLN C 440 ASN C 450 ASN C 564 GLN C 641 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.128543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.096475 restraints weight = 68553.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098980 restraints weight = 39658.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099641 restraints weight = 23523.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099796 restraints weight = 22174.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099795 restraints weight = 18726.090| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 26941 Z= 0.329 Angle : 0.891 20.574 36832 Z= 0.440 Chirality : 0.053 0.543 4378 Planarity : 0.006 0.062 4666 Dihedral : 8.720 111.386 4591 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.21 % Allowed : 15.40 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3304 helix: -0.36 (0.19), residues: 682 sheet: 0.03 (0.18), residues: 776 loop : -1.00 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 273 TYR 0.025 0.003 TYR L 91 PHE 0.028 0.003 PHE B 888 TRP 0.045 0.003 TRP H 103 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00759 (26854) covalent geometry : angle 0.82655 (36611) SS BOND : bond 0.00597 ( 40) SS BOND : angle 2.71154 ( 80) hydrogen bonds : bond 0.05049 ( 949) hydrogen bonds : angle 6.53450 ( 2658) link_BETA1-4 : bond 0.00665 ( 11) link_BETA1-4 : angle 2.24116 ( 33) link_NAG-ASN : bond 0.00833 ( 36) link_NAG-ASN : angle 5.68326 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 268 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7539 (mpp) REVERT: A 742 ILE cc_start: 0.9542 (mm) cc_final: 0.9232 (tt) REVERT: A 759 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8552 (t80) REVERT: B 58 PHE cc_start: 0.8516 (m-80) cc_final: 0.8230 (m-10) REVERT: B 134 GLN cc_start: 0.7828 (tp40) cc_final: 0.7153 (tp40) REVERT: B 204 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.5795 (m-80) REVERT: B 583 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 584 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7559 (pt) REVERT: B 983 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7371 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8088 (tp40) REVERT: C 223 LEU cc_start: 0.6984 (tp) cc_final: 0.6711 (tp) REVERT: C 265 TYR cc_start: 0.6503 (p90) cc_final: 0.6277 (p90) REVERT: C 574 ASP cc_start: 0.6862 (m-30) cc_final: 0.6592 (p0) REVERT: C 731 MET cc_start: 0.8597 (ptp) cc_final: 0.8197 (ptp) REVERT: C 918 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: H 50 TRP cc_start: 0.5177 (t60) cc_final: 0.4611 (t60) REVERT: H 59 TYR cc_start: 0.6686 (m-80) cc_final: 0.5714 (m-80) REVERT: H 64 GLN cc_start: 0.8117 (tp40) cc_final: 0.7763 (mm-40) REVERT: H 69 MET cc_start: 0.7909 (mpp) cc_final: 0.7560 (mpp) REVERT: R 96 TYR cc_start: 0.7999 (t80) cc_final: 0.7721 (t80) REVERT: R 101 ASP cc_start: 0.7885 (m-30) cc_final: 0.7314 (m-30) REVERT: L 39 LYS cc_start: 0.8048 (tptt) cc_final: 0.7579 (mptt) REVERT: L 91 TYR cc_start: 0.8133 (p90) cc_final: 0.7753 (p90) REVERT: S 54 ARG cc_start: 0.5971 (ptp90) cc_final: 0.5302 (ptp-170) outliers start: 144 outliers final: 101 residues processed: 384 average time/residue: 0.1392 time to fit residues: 90.5367 Evaluate side-chains 347 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 240 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 223 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 310 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 901 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 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 = 0.4060 r_free = 0.4060 target = 0.137224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105733 restraints weight = 72339.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.108521 restraints weight = 37059.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110359 restraints weight = 23335.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111498 restraints weight = 16940.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112281 restraints weight = 13698.901| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26941 Z= 0.142 Angle : 0.757 20.619 36832 Z= 0.364 Chirality : 0.049 0.459 4378 Planarity : 0.005 0.062 4666 Dihedral : 7.940 107.621 4591 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.69 % Allowed : 18.04 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.73 (0.14), residues: 3304 helix: -0.12 (0.19), residues: 687 sheet: 0.15 (0.18), residues: 767 loop : -0.87 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 95 TYR 0.030 0.002 TYR B 904 PHE 0.027 0.002 PHE C 168 TRP 0.035 0.002 TRP H 103 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00318 (26854) covalent geometry : angle 0.68410 (36611) SS BOND : bond 0.00393 ( 40) SS BOND : angle 2.36909 ( 80) hydrogen bonds : bond 0.03998 ( 949) hydrogen bonds : angle 6.09696 ( 2658) link_BETA1-4 : bond 0.00562 ( 11) link_BETA1-4 : angle 2.01246 ( 33) link_NAG-ASN : bond 0.00780 ( 36) link_NAG-ASN : angle 5.61167 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 298 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 ASP cc_start: 0.7630 (p0) cc_final: 0.5863 (p0) REVERT: A 740 MET cc_start: 0.7894 (mpp) cc_final: 0.7019 (mpt) REVERT: A 742 ILE cc_start: 0.9440 (mm) cc_final: 0.9149 (tt) REVERT: A 759 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8264 (t80) REVERT: A 819 GLU cc_start: 0.7967 (pt0) cc_final: 0.7406 (pt0) REVERT: A 1092 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7722 (mt-10) REVERT: B 49 HIS cc_start: 0.7066 (t-170) cc_final: 0.6625 (t-170) REVERT: B 58 PHE cc_start: 0.8213 (m-80) cc_final: 0.7575 (m-10) REVERT: B 129 LYS cc_start: 0.7241 (tptm) cc_final: 0.6933 (tptm) REVERT: B 134 GLN cc_start: 0.7466 (tp40) cc_final: 0.6736 (tp40) REVERT: B 409 GLN cc_start: 0.8330 (tt0) cc_final: 0.8072 (tt0) REVERT: B 584 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7478 (pt) REVERT: B 983 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7175 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8505 (tp-100) cc_final: 0.7934 (tp40) REVERT: C 223 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6660 (tp) REVERT: C 265 TYR cc_start: 0.6792 (p90) cc_final: 0.6572 (p90) REVERT: C 452 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7339 (mp) REVERT: C 780 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: C 887 THR cc_start: 0.8335 (p) cc_final: 0.8118 (p) REVERT: C 918 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: H 29 PHE cc_start: 0.8349 (t80) cc_final: 0.8134 (t80) REVERT: H 59 TYR cc_start: 0.6389 (m-80) cc_final: 0.5644 (m-80) REVERT: H 64 GLN cc_start: 0.8027 (tp40) cc_final: 0.7819 (mm-40) REVERT: R 101 ASP cc_start: 0.8275 (m-30) cc_final: 0.7978 (m-30) REVERT: L 39 LYS cc_start: 0.8037 (tptt) cc_final: 0.7682 (mmtp) REVERT: S 78 LEU cc_start: 0.1239 (OUTLIER) cc_final: 0.1026 (mm) outliers start: 102 outliers final: 68 residues processed: 379 average time/residue: 0.1433 time to fit residues: 91.5413 Evaluate side-chains 338 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 262 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 120 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 285 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 66 optimal weight: 0.0970 chunk 148 optimal weight: 5.9990 chunk 263 optimal weight: 0.0980 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 233 optimal weight: 0.0030 chunk 121 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 895 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 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 = 0.4077 r_free = 0.4077 target = 0.133815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101554 restraints weight = 66610.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104939 restraints weight = 37983.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106904 restraints weight = 21815.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107166 restraints weight = 16519.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.107397 restraints weight = 14508.382| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 26941 Z= 0.131 Angle : 0.735 20.374 36832 Z= 0.353 Chirality : 0.048 0.417 4378 Planarity : 0.005 0.064 4666 Dihedral : 7.431 106.470 4591 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.90 % Allowed : 18.62 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.59 (0.14), residues: 3304 helix: -0.02 (0.19), residues: 681 sheet: 0.31 (0.18), residues: 754 loop : -0.81 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 95 TYR 0.022 0.001 TYR B 904 PHE 0.022 0.002 PHE B 888 TRP 0.025 0.001 TRP H 103 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00296 (26854) covalent geometry : angle 0.66634 (36611) SS BOND : bond 0.00362 ( 40) SS BOND : angle 2.02532 ( 80) hydrogen bonds : bond 0.03813 ( 949) hydrogen bonds : angle 5.91972 ( 2658) link_BETA1-4 : bond 0.00461 ( 11) link_BETA1-4 : angle 1.91978 ( 33) link_NAG-ASN : bond 0.00769 ( 36) link_NAG-ASN : angle 5.45263 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 300 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7783 (t80) cc_final: 0.7294 (t80) REVERT: A 737 ASP cc_start: 0.7582 (p0) cc_final: 0.5913 (p0) REVERT: A 740 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.6790 (mpt) REVERT: A 742 ILE cc_start: 0.9389 (mm) cc_final: 0.9142 (tt) REVERT: A 759 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8182 (t80) REVERT: A 902 MET cc_start: 0.8417 (tpt) cc_final: 0.7783 (tpt) REVERT: B 134 GLN cc_start: 0.7577 (tp40) cc_final: 0.6891 (tp40) REVERT: B 189 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 290 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.6356 (p0) REVERT: B 409 GLN cc_start: 0.8305 (tt0) cc_final: 0.7615 (tt0) REVERT: B 983 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7354 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7775 (tp-100) REVERT: C 223 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6685 (tp) REVERT: C 265 TYR cc_start: 0.6800 (p90) cc_final: 0.6597 (p90) REVERT: C 452 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7349 (mp) REVERT: C 577 ARG cc_start: 0.7209 (ttm170) cc_final: 0.6801 (mtm180) REVERT: C 780 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7249 (pm20) REVERT: C 918 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: C 1061 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9020 (m) REVERT: H 59 TYR cc_start: 0.6567 (m-80) cc_final: 0.5643 (m-80) REVERT: H 64 GLN cc_start: 0.8093 (tp40) cc_final: 0.7771 (mm-40) REVERT: H 103 TRP cc_start: 0.6587 (m100) cc_final: 0.6313 (m100) REVERT: R 96 TYR cc_start: 0.7728 (t80) cc_final: 0.7361 (t80) REVERT: R 101 ASP cc_start: 0.8271 (m-30) cc_final: 0.7936 (m-30) REVERT: L 39 LYS cc_start: 0.8115 (tptt) cc_final: 0.7656 (mmtp) REVERT: L 93 SER cc_start: 0.7418 (OUTLIER) cc_final: 0.7160 (t) REVERT: S 79 GLU cc_start: 0.8095 (tp30) cc_final: 0.7673 (tp30) outliers start: 108 outliers final: 76 residues processed: 387 average time/residue: 0.1412 time to fit residues: 92.0718 Evaluate side-chains 359 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 272 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 303 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 276 optimal weight: 0.8980 chunk 228 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.105726 restraints weight = 73161.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108542 restraints weight = 42880.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109897 restraints weight = 23679.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110738 restraints weight = 17531.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.110823 restraints weight = 15320.509| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26941 Z= 0.180 Angle : 0.751 20.374 36832 Z= 0.365 Chirality : 0.049 0.408 4378 Planarity : 0.005 0.061 4666 Dihedral : 7.372 107.658 4591 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.94 % Allowed : 19.38 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.65 (0.14), residues: 3304 helix: -0.05 (0.19), residues: 685 sheet: 0.14 (0.18), residues: 779 loop : -0.80 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 95 TYR 0.024 0.002 TYR B 904 PHE 0.028 0.002 PHE B 888 TRP 0.022 0.002 TRP H 103 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00415 (26854) covalent geometry : angle 0.68433 (36611) SS BOND : bond 0.00376 ( 40) SS BOND : angle 2.15246 ( 80) hydrogen bonds : bond 0.04003 ( 949) hydrogen bonds : angle 6.00143 ( 2658) link_BETA1-4 : bond 0.00458 ( 11) link_BETA1-4 : angle 1.90259 ( 33) link_NAG-ASN : bond 0.00740 ( 36) link_NAG-ASN : angle 5.41152 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 277 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASN cc_start: 0.6944 (m110) cc_final: 0.6449 (t0) REVERT: A 220 PHE cc_start: 0.7847 (t80) cc_final: 0.7372 (t80) REVERT: A 759 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8271 (t80) REVERT: A 902 MET cc_start: 0.8460 (tpt) cc_final: 0.7838 (tpt) REVERT: B 58 PHE cc_start: 0.8439 (m-80) cc_final: 0.8110 (m-80) REVERT: B 129 LYS cc_start: 0.7158 (tptm) cc_final: 0.6893 (tptm) REVERT: B 134 GLN cc_start: 0.7516 (tp40) cc_final: 0.6803 (tp40) REVERT: B 189 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8097 (mm) REVERT: B 203 ILE cc_start: 0.8327 (pt) cc_final: 0.8110 (mt) REVERT: B 290 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.6203 (p0) REVERT: B 409 GLN cc_start: 0.8364 (tt0) cc_final: 0.7686 (tt0) REVERT: B 664 ILE cc_start: 0.8534 (mm) cc_final: 0.8314 (mt) REVERT: B 983 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7254 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8561 (tp-100) cc_final: 0.7988 (tp40) REVERT: C 223 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6654 (tp) REVERT: C 265 TYR cc_start: 0.6824 (p90) cc_final: 0.6573 (p90) REVERT: C 452 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7614 (mp) REVERT: C 577 ARG cc_start: 0.7209 (ttm170) cc_final: 0.6842 (mtm180) REVERT: C 731 MET cc_start: 0.8414 (ptp) cc_final: 0.7817 (ptp) REVERT: C 774 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8162 (mm-40) REVERT: C 780 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: C 918 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: C 1061 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.8888 (m) REVERT: H 50 TRP cc_start: 0.5270 (t60) cc_final: 0.4671 (t60) REVERT: H 59 TYR cc_start: 0.6452 (m-80) cc_final: 0.5710 (m-80) REVERT: H 64 GLN cc_start: 0.8016 (tp40) cc_final: 0.7748 (mm-40) REVERT: H 69 MET cc_start: 0.7664 (mpp) cc_final: 0.7460 (mpp) REVERT: H 103 TRP cc_start: 0.6401 (m100) cc_final: 0.6098 (m100) REVERT: R 96 TYR cc_start: 0.7730 (t80) cc_final: 0.7492 (t80) REVERT: R 101 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: L 4 LEU cc_start: 0.8147 (mm) cc_final: 0.7425 (pt) REVERT: L 39 LYS cc_start: 0.8137 (tptt) cc_final: 0.7617 (mptt) REVERT: L 93 SER cc_start: 0.7280 (OUTLIER) cc_final: 0.7048 (t) REVERT: S 79 GLU cc_start: 0.8016 (tp30) cc_final: 0.7711 (tp30) outliers start: 109 outliers final: 86 residues processed: 361 average time/residue: 0.1404 time to fit residues: 85.3845 Evaluate side-chains 366 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 269 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 29 optimal weight: 20.0000 chunk 224 optimal weight: 0.4980 chunk 293 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 323 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 196 optimal weight: 0.3980 chunk 249 optimal weight: 8.9990 chunk 333 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 409 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 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 = 0.4086 r_free = 0.4086 target = 0.137734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106935 restraints weight = 72708.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.110687 restraints weight = 37498.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.111813 restraints weight = 21317.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.113141 restraints weight = 15611.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.113244 restraints weight = 12675.069| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26941 Z= 0.129 Angle : 0.725 20.262 36832 Z= 0.350 Chirality : 0.048 0.399 4378 Planarity : 0.005 0.060 4666 Dihedral : 7.065 105.939 4591 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.25 % Allowed : 20.25 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.56 (0.14), residues: 3304 helix: 0.02 (0.19), residues: 687 sheet: 0.21 (0.18), residues: 768 loop : -0.74 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 95 TYR 0.020 0.001 TYR B 904 PHE 0.028 0.002 PHE B 888 TRP 0.024 0.001 TRP H 103 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00288 (26854) covalent geometry : angle 0.66218 (36611) SS BOND : bond 0.00361 ( 40) SS BOND : angle 1.93247 ( 80) hydrogen bonds : bond 0.03682 ( 949) hydrogen bonds : angle 5.82499 ( 2658) link_BETA1-4 : bond 0.00506 ( 11) link_BETA1-4 : angle 1.85443 ( 33) link_NAG-ASN : bond 0.00800 ( 36) link_NAG-ASN : angle 5.18197 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 290 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7806 (t80) cc_final: 0.7354 (t80) REVERT: A 742 ILE cc_start: 0.9423 (mm) cc_final: 0.9156 (tt) REVERT: A 759 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8126 (t80) REVERT: A 819 GLU cc_start: 0.8158 (pt0) cc_final: 0.7530 (pt0) REVERT: A 902 MET cc_start: 0.8366 (tpt) cc_final: 0.7729 (tpt) REVERT: A 1092 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7222 (pm20) REVERT: B 49 HIS cc_start: 0.6948 (t-170) cc_final: 0.6557 (t-170) REVERT: B 58 PHE cc_start: 0.8374 (m-80) cc_final: 0.8023 (m-80) REVERT: B 129 LYS cc_start: 0.7161 (tptm) cc_final: 0.6878 (tptm) REVERT: B 134 GLN cc_start: 0.7561 (tp40) cc_final: 0.6872 (tp40) REVERT: B 189 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8109 (mm) REVERT: B 203 ILE cc_start: 0.8326 (pt) cc_final: 0.8072 (mt) REVERT: B 229 LEU cc_start: 0.8379 (mt) cc_final: 0.8177 (mp) REVERT: B 290 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.6161 (p0) REVERT: B 409 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: B 587 ILE cc_start: 0.6586 (mt) cc_final: 0.6229 (mp) REVERT: B 983 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7232 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8436 (tp-100) cc_final: 0.7778 (tp-100) REVERT: C 223 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6663 (tp) REVERT: C 265 TYR cc_start: 0.6882 (p90) cc_final: 0.6629 (p90) REVERT: C 452 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7485 (mp) REVERT: C 577 ARG cc_start: 0.7213 (ttm170) cc_final: 0.6794 (mtm180) REVERT: C 731 MET cc_start: 0.8329 (ptp) cc_final: 0.7705 (ptp) REVERT: C 774 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8129 (mm-40) REVERT: C 780 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: C 918 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: C 1055 SER cc_start: 0.9133 (t) cc_final: 0.8756 (p) REVERT: C 1061 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.9019 (m) REVERT: H 50 TRP cc_start: 0.5004 (t60) cc_final: 0.4393 (t60) REVERT: H 56 ASN cc_start: 0.7928 (m110) cc_final: 0.7282 (m-40) REVERT: H 59 TYR cc_start: 0.6399 (m-80) cc_final: 0.5671 (m-80) REVERT: H 64 GLN cc_start: 0.8045 (tp40) cc_final: 0.7741 (mm-40) REVERT: H 103 TRP cc_start: 0.6406 (m100) cc_final: 0.6186 (m100) REVERT: R 102 CYS cc_start: 0.5902 (t) cc_final: 0.5652 (t) REVERT: L 33 LEU cc_start: 0.8269 (tp) cc_final: 0.7696 (mt) REVERT: L 39 LYS cc_start: 0.8172 (tptt) cc_final: 0.7640 (mptt) REVERT: L 71 PHE cc_start: 0.7566 (m-10) cc_final: 0.7324 (m-10) REVERT: L 90 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8581 (tm-30) REVERT: S 79 GLU cc_start: 0.7963 (tp30) cc_final: 0.7681 (tp30) outliers start: 90 outliers final: 69 residues processed: 360 average time/residue: 0.1485 time to fit residues: 89.2526 Evaluate side-chains 348 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 268 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 225 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 329 optimal weight: 0.0370 chunk 159 optimal weight: 0.9990 chunk 286 optimal weight: 0.0970 chunk 120 optimal weight: 0.0060 chunk 271 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.139941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109394 restraints weight = 72387.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.113024 restraints weight = 38843.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.114240 restraints weight = 22389.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115242 restraints weight = 16303.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.115449 restraints weight = 13506.974| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26941 Z= 0.122 Angle : 0.717 20.211 36832 Z= 0.345 Chirality : 0.047 0.383 4378 Planarity : 0.005 0.062 4666 Dihedral : 6.879 105.230 4590 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.89 % Allowed : 20.79 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.49 (0.14), residues: 3304 helix: 0.09 (0.20), residues: 676 sheet: 0.29 (0.18), residues: 753 loop : -0.70 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1107 TYR 0.022 0.001 TYR A 369 PHE 0.028 0.001 PHE B 888 TRP 0.024 0.001 TRP H 103 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00268 (26854) covalent geometry : angle 0.65614 (36611) SS BOND : bond 0.00321 ( 40) SS BOND : angle 1.81227 ( 80) hydrogen bonds : bond 0.03583 ( 949) hydrogen bonds : angle 5.71176 ( 2658) link_BETA1-4 : bond 0.00492 ( 11) link_BETA1-4 : angle 1.81287 ( 33) link_NAG-ASN : bond 0.00787 ( 36) link_NAG-ASN : angle 5.11694 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 290 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7813 (t80) cc_final: 0.7331 (t80) REVERT: A 742 ILE cc_start: 0.9412 (mm) cc_final: 0.9144 (tt) REVERT: A 902 MET cc_start: 0.8279 (tpt) cc_final: 0.7652 (tpt) REVERT: A 1092 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7201 (pm20) REVERT: B 58 PHE cc_start: 0.8402 (m-80) cc_final: 0.8066 (m-80) REVERT: B 129 LYS cc_start: 0.7183 (tptm) cc_final: 0.6903 (tptm) REVERT: B 134 GLN cc_start: 0.7591 (tp40) cc_final: 0.6914 (tp40) REVERT: B 290 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.6243 (p0) REVERT: B 587 ILE cc_start: 0.6535 (mt) cc_final: 0.6190 (mp) REVERT: B 664 ILE cc_start: 0.8341 (mm) cc_final: 0.7906 (mt) REVERT: B 919 ASN cc_start: 0.7859 (t0) cc_final: 0.7567 (t0) REVERT: B 983 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7237 (ttp-170) REVERT: B 1010 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7769 (tp-100) REVERT: C 223 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6699 (tp) REVERT: C 265 TYR cc_start: 0.6825 (p90) cc_final: 0.6559 (p90) REVERT: C 452 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7524 (mp) REVERT: C 577 ARG cc_start: 0.7062 (ttm170) cc_final: 0.6691 (mtm180) REVERT: C 731 MET cc_start: 0.8304 (ptp) cc_final: 0.7714 (ptp) REVERT: C 780 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: C 918 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: C 1055 SER cc_start: 0.9131 (t) cc_final: 0.8740 (p) REVERT: C 1061 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9024 (m) REVERT: H 59 TYR cc_start: 0.6442 (m-80) cc_final: 0.5797 (m-80) REVERT: H 64 GLN cc_start: 0.8064 (tp40) cc_final: 0.7778 (mm-40) REVERT: H 100 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.5068 (t80) REVERT: H 103 TRP cc_start: 0.6476 (m100) cc_final: 0.6261 (m100) REVERT: R 101 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6344 (m-30) REVERT: L 39 LYS cc_start: 0.8155 (tptt) cc_final: 0.7755 (mmtt) REVERT: L 71 PHE cc_start: 0.7553 (m-10) cc_final: 0.7158 (m-10) REVERT: L 90 GLN cc_start: 0.8989 (pp30) cc_final: 0.8751 (tm-30) REVERT: S 79 GLU cc_start: 0.8029 (tp30) cc_final: 0.7736 (tp30) outliers start: 80 outliers final: 61 residues processed: 356 average time/residue: 0.1482 time to fit residues: 88.5802 Evaluate side-chains 339 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 269 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain R residue 27 TYR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 229 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 320 optimal weight: 10.0000 chunk 323 optimal weight: 8.9990 chunk 292 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 192 optimal weight: 0.0000 chunk 116 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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 = 0.4063 r_free = 0.4063 target = 0.134103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101449 restraints weight = 66269.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104567 restraints weight = 39528.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105057 restraints weight = 24352.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105527 restraints weight = 19227.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105729 restraints weight = 17239.756| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26941 Z= 0.179 Angle : 0.740 20.286 36832 Z= 0.360 Chirality : 0.048 0.380 4378 Planarity : 0.005 0.059 4666 Dihedral : 7.000 107.148 4590 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.15 % Allowed : 21.08 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3304 helix: 0.13 (0.20), residues: 677 sheet: 0.15 (0.18), residues: 765 loop : -0.75 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1107 TYR 0.020 0.001 TYR B 904 PHE 0.027 0.002 PHE B 888 TRP 0.021 0.001 TRP H 103 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00413 (26854) covalent geometry : angle 0.68010 (36611) SS BOND : bond 0.00376 ( 40) SS BOND : angle 1.91350 ( 80) hydrogen bonds : bond 0.03878 ( 949) hydrogen bonds : angle 5.81377 ( 2658) link_BETA1-4 : bond 0.00423 ( 11) link_BETA1-4 : angle 1.88358 ( 33) link_NAG-ASN : bond 0.00734 ( 36) link_NAG-ASN : angle 5.12188 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4224.28 seconds wall clock time: 74 minutes 2.16 seconds (4442.16 seconds total)