Starting phenix.real_space_refine on Sat Jul 4 20:04:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uhc_26512/07_2026/7uhc_26512.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uhc_26512/07_2026/7uhc_26512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uhc_26512/07_2026/7uhc_26512.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uhc_26512/07_2026/7uhc_26512.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uhc_26512/07_2026/7uhc_26512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uhc_26512/07_2026/7uhc_26512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uhc_26512/07_2026/7uhc_26512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uhc_26512/07_2026/7uhc_26512.map" } resolution = 3.1 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= -0.001 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 14754 2.51 5 N 3927 2.21 5 O 4353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23136 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7058 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 7 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 871 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ASN:plan1': 21, 'GLU:plan': 22, 'ASP:plan': 22, 'GLN:plan1': 10, 'PHE:plan': 5, 'ARG:plan': 7, 'TYR:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 390 Chain: "K" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "B" Number of atoms: 7058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7058 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 7 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 871 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ASN:plan1': 21, 'GLU:plan': 22, 'ASP:plan': 22, 'GLN:plan1': 10, 'PHE:plan': 5, 'ARG:plan': 7, 'TYR:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 390 Chain: "C" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 7058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7058 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 53, 'TRANS': 935} Chain breaks: 7 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 871 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ASN:plan1': 21, 'GLU:plan': 22, 'ASP:plan': 22, 'GLN:plan1': 10, 'PHE:plan': 5, 'ARG:plan': 7, 'TYR:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 390 Chain: "E" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 374 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 74} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.35, per 1000 atoms: 0.27 Number of scatterers: 23136 At special positions: 0 Unit cell: (131.393, 134.402, 197.591, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 4353 8.00 N 3927 7.00 C 14754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.08 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.00 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.09 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.11 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.07 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.08 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.00 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=2.09 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.11 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.07 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.08 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.00 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.09 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.11 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.01 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.07 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 343 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 234 " " NAG D1304 " - " ASN D 282 " " NAG D1305 " - " ASN D 331 " " NAG D1306 " - " ASN D 603 " " NAG D1307 " - " ASN D 616 " " NAG D1308 " - " ASN D 657 " " NAG D1309 " - " ASN D 709 " " NAG D1310 " - " ASN D1074 " " NAG D1311 " - " ASN D 165 " " NAG D1312 " - " ASN D 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN D 717 " " NAG P 1 " - " ASN D 801 " " NAG Q 1 " - " ASN D1098 " " NAG R 1 " - " ASN D1134 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 42 sheets defined 30.4% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.548A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.855A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.012A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.909A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.638A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.766A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.345A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.031A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 Processing helix chain 'K' and resid 25 through 48 Processing helix chain 'K' and resid 51 through 74 removed outlier: 3.594A pdb=" N GLU K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU K 72 " --> pdb=" O HIS K 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.548A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.855A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.011A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.638A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.766A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.345A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.031A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 25 through 48 Processing helix chain 'C' and resid 51 through 74 removed outlier: 3.593A pdb=" N GLU C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.548A pdb=" N ASN D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.856A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 386 through 390 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.012A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 823 removed outlier: 3.638A pdb=" N PHE D 823 " --> pdb=" O GLU D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 919 Processing helix chain 'D' and resid 919 through 940 removed outlier: 3.766A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 944 Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.345A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 5.031A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 Processing helix chain 'E' and resid 25 through 48 Processing helix chain 'E' and resid 51 through 74 removed outlier: 3.593A pdb=" N GLU E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.280A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.011A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.450A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.570A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.255A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.596A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE A 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.475A pdb=" N ALA A 701 " --> pdb=" O ILE D 788 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LYS D 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN A 703 " --> pdb=" O LYS D 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.277A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.280A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.011A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.451A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.570A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.255A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.277A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.919A pdb=" N ILE B 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.280A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 48 through 55 removed outlier: 7.450A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.570A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.255A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.277A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1120 through 1122 1198 hydrogen bonds defined for protein. 3297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3976 1.32 - 1.45: 6156 1.45 - 1.58: 13355 1.58 - 1.70: 3 1.70 - 1.83: 126 Bond restraints: 23616 Sorted by residual: bond pdb=" C CYS B 662 " pdb=" O CYS B 662 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.20e-02 6.94e+03 1.49e+01 bond pdb=" C CYS D 662 " pdb=" O CYS D 662 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.20e-02 6.94e+03 1.48e+01 bond pdb=" C CYS A 662 " pdb=" O CYS A 662 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.20e-02 6.94e+03 1.48e+01 bond pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.80e+00 bond pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.70e+00 ... (remaining 23611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.46: 32249 6.46 - 12.91: 106 12.91 - 19.37: 0 19.37 - 25.83: 3 25.83 - 32.28: 3 Bond angle restraints: 32361 Sorted by residual: angle pdb=" C2 NAG G 1 " pdb=" N2 NAG G 1 " pdb=" C7 NAG G 1 " ideal model delta sigma weight residual 124.56 156.84 -32.28 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C2 NAG L 1 " pdb=" N2 NAG L 1 " pdb=" C7 NAG L 1 " ideal model delta sigma weight residual 124.56 156.83 -32.27 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 156.82 -32.26 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C LEU D 861 " pdb=" N PRO D 862 " pdb=" CA PRO D 862 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.01e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.44 -6.78 7.20e-01 1.93e+00 8.88e+01 ... (remaining 32356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 13021 17.61 - 35.23: 320 35.23 - 52.84: 63 52.84 - 70.45: 27 70.45 - 88.07: 21 Dihedral angle restraints: 13452 sinusoidal: 4185 harmonic: 9267 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -152.39 66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS D1082 " pdb=" SG CYS D1082 " pdb=" SG CYS D1126 " pdb=" CB CYS D1126 " ideal model delta sinusoidal sigma weight residual -86.00 -152.38 66.38 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -152.38 66.38 1 1.00e+01 1.00e-02 5.75e+01 ... (remaining 13449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3405 0.101 - 0.203: 456 0.203 - 0.304: 108 0.304 - 0.406: 33 0.406 - 0.507: 3 Chirality restraints: 4005 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.33e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.24e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.24e+01 ... (remaining 4002 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 709 " 0.026 2.00e-02 2.50e+03 2.71e-02 9.15e+00 pdb=" CG ASN D 709 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN D 709 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 709 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG D1309 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.026 2.00e-02 2.50e+03 2.70e-02 9.09e+00 pdb=" CG ASN B 709 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.026 2.00e-02 2.50e+03 2.70e-02 9.08e+00 pdb=" CG ASN A 709 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.033 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 13344 3.02 - 3.49: 21050 3.49 - 3.96: 36074 3.96 - 4.43: 40491 4.43 - 4.90: 65525 Nonbonded interactions: 176484 Sorted by model distance: nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.551 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.551 3.120 nonbonded pdb=" NZ LYS D 811 " pdb=" OD2 ASP D 820 " model vdw 2.552 3.120 nonbonded pdb=" O GLY D 908 " pdb=" NZ LYS D1038 " model vdw 2.571 3.120 nonbonded pdb=" O GLY A 908 " pdb=" NZ LYS A1038 " model vdw 2.572 3.120 ... (remaining 176479 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.650 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.011 0.081 23715 Z= 0.600 Angle : 1.343 32.284 32619 Z= 0.881 Chirality : 0.082 0.507 4005 Planarity : 0.005 0.025 4182 Dihedral : 9.985 88.067 7335 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.32 % Rotamer: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.06 % 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: 0.29 (0.13), residues: 3138 helix: 0.58 (0.16), residues: 837 sheet: 0.96 (0.18), residues: 708 loop : -0.30 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.022 0.004 TYR D 489 PHE 0.018 0.003 PHE A 898 TRP 0.012 0.004 TRP D 353 HIS 0.003 0.001 HIS D1083 Details of bonding type rmsd/Z covalent geometry : bond 0.01031 / 0.58 (23616) covalent geometry : angle 1.33045 / 0.88 (32361) SS BOND : bond 0.03538 / 2.24 ( 39) SS BOND : angle 2.90522 / 1.87 ( 78) hydrogen bonds : bond 0.17945 / 12.02 ( 1162) hydrogen bonds : angle 8.06886 / 5.70 ( 3297) link_BETA1-4 : bond 0.05622 / 3.32 ( 12) link_BETA1-4 : angle 2.47865 / 1.55 ( 36) link_NAG-ASN : bond 0.05782 / 3.54 ( 48) link_NAG-ASN : angle 2.20080 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 303 time to evaluate : 0.752 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 309 average time/residue: 0.1762 time to fit residues: 82.6502 Evaluate side-chains 136 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain D residue 616 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.0040 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN A 804 GLN A 935 GLN A1048 HIS A1071 GLN B 784 GLN B 804 GLN B 907 ASN B 913 GLN B 935 GLN B1048 HIS B1071 GLN D 804 GLN D 907 ASN D 913 GLN D 935 GLN D1002 GLN D1048 HIS D1071 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.138879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.090437 restraints weight = 39975.700| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.13 r_work: 0.3138 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23715 Z= 0.134 Angle : 0.581 8.785 32619 Z= 0.304 Chirality : 0.045 0.188 4005 Planarity : 0.004 0.038 4182 Dihedral : 4.398 58.682 3348 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.46 % Allowed : 5.73 % Favored : 92.81 % 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: 1.25 (0.14), residues: 3138 helix: 2.42 (0.18), residues: 837 sheet: 1.25 (0.19), residues: 684 loop : -0.19 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.021 0.001 TYR A1067 PHE 0.016 0.001 PHE B 400 TRP 0.012 0.001 TRP A 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (23616) covalent geometry : angle 0.56128 / 0.30 (32361) SS BOND : bond 0.00167 / 0.10 ( 39) SS BOND : angle 1.09160 / 0.73 ( 78) hydrogen bonds : bond 0.05574 / 3.84 ( 1162) hydrogen bonds : angle 5.83083 / 4.14 ( 3297) link_BETA1-4 : bond 0.00523 / 0.31 ( 12) link_BETA1-4 : angle 1.52498 / 0.94 ( 36) link_NAG-ASN : bond 0.00629 / 0.35 ( 48) link_NAG-ASN : angle 2.08928 / 1.36 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8328 (tt0) REVERT: A 1135 ASN cc_start: 0.8411 (t0) cc_final: 0.8199 (t0) REVERT: B 320 VAL cc_start: 0.8512 (t) cc_final: 0.8161 (p) REVERT: B 353 TRP cc_start: 0.8378 (p-90) cc_final: 0.8146 (p-90) REVERT: B 365 TYR cc_start: 0.7742 (m-80) cc_final: 0.7126 (m-80) REVERT: D 41 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7889 (mtpp) REVERT: D 353 TRP cc_start: 0.8410 (p-90) cc_final: 0.8197 (p-90) REVERT: D 697 MET cc_start: 0.9220 (ptm) cc_final: 0.8960 (ptp) outliers start: 28 outliers final: 10 residues processed: 178 average time/residue: 0.1308 time to fit residues: 39.2280 Evaluate side-chains 139 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 980 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 309 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 HIS A 755 GLN A1002 GLN B 655 HIS B 755 GLN B 913 GLN D 655 HIS D 703 ASN D 755 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082847 restraints weight = 39302.260| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.20 r_work: 0.2916 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 23715 Z= 0.293 Angle : 0.644 8.398 32619 Z= 0.333 Chirality : 0.048 0.180 4005 Planarity : 0.005 0.043 4182 Dihedral : 4.433 55.246 3348 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.61 % Allowed : 6.67 % Favored : 91.72 % 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: 1.04 (0.14), residues: 3138 helix: 2.32 (0.18), residues: 846 sheet: 0.97 (0.19), residues: 678 loop : -0.30 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1019 TYR 0.022 0.002 TYR A1067 PHE 0.025 0.002 PHE A 92 TRP 0.017 0.002 TRP A 353 HIS 0.008 0.002 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.29 (23616) covalent geometry : angle 0.63017 / 0.33 (32361) SS BOND : bond 0.00471 / 0.25 ( 39) SS BOND : angle 0.83860 / 0.57 ( 78) hydrogen bonds : bond 0.05433 / 3.71 ( 1162) hydrogen bonds : angle 5.46242 / 3.88 ( 3297) link_BETA1-4 : bond 0.00458 / 0.27 ( 12) link_BETA1-4 : angle 0.93930 / 0.58 ( 36) link_NAG-ASN : bond 0.00553 / 0.32 ( 48) link_NAG-ASN : angle 1.99541 / 1.32 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8143 (t70) cc_final: 0.7932 (t70) REVERT: A 534 VAL cc_start: 0.9073 (t) cc_final: 0.8830 (p) REVERT: A 979 ASP cc_start: 0.8389 (m-30) cc_final: 0.8181 (m-30) REVERT: B 353 TRP cc_start: 0.8275 (p-90) cc_final: 0.8038 (p-90) REVERT: B 534 VAL cc_start: 0.9169 (t) cc_final: 0.8925 (p) REVERT: D 41 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7913 (mtpp) REVERT: D 353 TRP cc_start: 0.8218 (p-90) cc_final: 0.7953 (p-90) REVERT: D 1002 GLN cc_start: 0.8450 (tp40) cc_final: 0.8177 (tp40) outliers start: 31 outliers final: 18 residues processed: 160 average time/residue: 0.1365 time to fit residues: 36.0146 Evaluate side-chains 140 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 973 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 66 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 257 optimal weight: 1.9990 chunk 213 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 248 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 907 ASN B 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085977 restraints weight = 38821.261| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.17 r_work: 0.2966 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23715 Z= 0.116 Angle : 0.497 6.038 32619 Z= 0.259 Chirality : 0.044 0.171 4005 Planarity : 0.004 0.040 4182 Dihedral : 4.117 55.350 3348 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.30 % Allowed : 7.03 % Favored : 91.67 % 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: 1.22 (0.14), residues: 3138 helix: 2.70 (0.18), residues: 825 sheet: 1.07 (0.20), residues: 639 loop : -0.26 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 995 TYR 0.019 0.001 TYR B1067 PHE 0.012 0.001 PHE D 238 TRP 0.015 0.001 TRP A 353 HIS 0.002 0.000 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (23616) covalent geometry : angle 0.48549 / 0.26 (32361) SS BOND : bond 0.00239 / 0.13 ( 39) SS BOND : angle 0.63772 / 0.42 ( 78) hydrogen bonds : bond 0.04386 / 3.03 ( 1162) hydrogen bonds : angle 5.12703 / 3.63 ( 3297) link_BETA1-4 : bond 0.00358 / 0.23 ( 12) link_BETA1-4 : angle 0.83853 / 0.52 ( 36) link_NAG-ASN : bond 0.00335 / 0.19 ( 48) link_NAG-ASN : angle 1.63814 / 1.08 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8088 (t70) cc_final: 0.7882 (t70) REVERT: A 392 PHE cc_start: 0.6592 (m-80) cc_final: 0.6245 (m-80) REVERT: A 534 VAL cc_start: 0.9036 (t) cc_final: 0.8802 (p) REVERT: A 901 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8449 (pt0) REVERT: D 41 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7936 (mtpp) REVERT: D 353 TRP cc_start: 0.8037 (p-90) cc_final: 0.7811 (p-90) REVERT: D 1002 GLN cc_start: 0.8284 (tp40) cc_final: 0.8068 (tp-100) outliers start: 25 outliers final: 11 residues processed: 139 average time/residue: 0.1331 time to fit residues: 31.4963 Evaluate side-chains 127 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 186 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 138 optimal weight: 40.0000 chunk 150 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 139 optimal weight: 0.3980 chunk 16 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.131363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.083150 restraints weight = 39567.061| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.63 r_work: 0.2938 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23715 Z= 0.191 Angle : 0.523 5.923 32619 Z= 0.270 Chirality : 0.045 0.177 4005 Planarity : 0.004 0.039 4182 Dihedral : 4.092 54.714 3348 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.77 % Allowed : 7.29 % Favored : 90.94 % 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: 1.08 (0.15), residues: 3138 helix: 2.66 (0.18), residues: 834 sheet: 0.86 (0.20), residues: 678 loop : -0.39 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.021 0.001 TYR A1067 PHE 0.018 0.001 PHE B 906 TRP 0.025 0.002 TRP A 353 HIS 0.004 0.001 HIS D1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (23616) covalent geometry : angle 0.51298 / 0.27 (32361) SS BOND : bond 0.00336 / 0.18 ( 39) SS BOND : angle 0.58530 / 0.39 ( 78) hydrogen bonds : bond 0.04469 / 3.08 ( 1162) hydrogen bonds : angle 5.08480 / 3.60 ( 3297) link_BETA1-4 : bond 0.00364 / 0.21 ( 12) link_BETA1-4 : angle 0.73890 / 0.46 ( 36) link_NAG-ASN : bond 0.00324 / 0.19 ( 48) link_NAG-ASN : angle 1.59773 / 1.06 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 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 392 PHE cc_start: 0.6574 (m-80) cc_final: 0.6255 (m-80) REVERT: A 534 VAL cc_start: 0.9088 (t) cc_final: 0.8869 (p) REVERT: A 901 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8486 (pt0) REVERT: B 353 TRP cc_start: 0.8307 (p-90) cc_final: 0.8085 (p-90) REVERT: B 534 VAL cc_start: 0.9174 (t) cc_final: 0.8973 (p) REVERT: D 41 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7948 (mtpp) REVERT: D 353 TRP cc_start: 0.8066 (p-90) cc_final: 0.7822 (p-90) REVERT: D 534 VAL cc_start: 0.9147 (t) cc_final: 0.8912 (p) REVERT: D 957 GLN cc_start: 0.8257 (mt0) cc_final: 0.8049 (tp40) REVERT: D 1002 GLN cc_start: 0.8488 (tp40) cc_final: 0.8250 (tp40) outliers start: 34 outliers final: 18 residues processed: 149 average time/residue: 0.1395 time to fit residues: 35.3072 Evaluate side-chains 130 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 172 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 289 optimal weight: 0.6980 chunk 66 optimal weight: 0.0370 chunk 301 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086038 restraints weight = 39546.516| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.14 r_work: 0.3019 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23715 Z= 0.093 Angle : 0.459 5.816 32619 Z= 0.239 Chirality : 0.043 0.174 4005 Planarity : 0.004 0.040 4182 Dihedral : 3.841 54.840 3348 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.20 % Allowed : 8.44 % Favored : 90.36 % 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: 1.26 (0.15), residues: 3138 helix: 2.88 (0.18), residues: 837 sheet: 1.00 (0.20), residues: 666 loop : -0.33 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.019 0.001 TYR B1067 PHE 0.010 0.001 PHE D 238 TRP 0.023 0.001 TRP A 353 HIS 0.001 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (23616) covalent geometry : angle 0.45044 / 0.24 (32361) SS BOND : bond 0.00141 / 0.07 ( 39) SS BOND : angle 0.50164 / 0.33 ( 78) hydrogen bonds : bond 0.03736 / 2.59 ( 1162) hydrogen bonds : angle 4.80716 / 3.39 ( 3297) link_BETA1-4 : bond 0.00390 / 0.24 ( 12) link_BETA1-4 : angle 0.72067 / 0.46 ( 36) link_NAG-ASN : bond 0.00479 / 0.26 ( 48) link_NAG-ASN : angle 1.38727 / 0.91 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6600 (m-80) cc_final: 0.6291 (m-80) REVERT: B 365 TYR cc_start: 0.8232 (m-80) cc_final: 0.7745 (m-80) REVERT: D 41 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7905 (mtpp) REVERT: D 269 TYR cc_start: 0.7917 (m-10) cc_final: 0.7426 (m-10) REVERT: D 697 MET cc_start: 0.9210 (ptm) cc_final: 0.8988 (ptp) REVERT: D 1002 GLN cc_start: 0.8280 (tp40) cc_final: 0.8066 (tp40) outliers start: 23 outliers final: 14 residues processed: 147 average time/residue: 0.1293 time to fit residues: 33.1215 Evaluate side-chains 124 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 260 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 180 optimal weight: 0.8980 chunk 284 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.086125 restraints weight = 38940.579| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.13 r_work: 0.2994 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23715 Z= 0.115 Angle : 0.465 5.866 32619 Z= 0.241 Chirality : 0.044 0.172 4005 Planarity : 0.004 0.036 4182 Dihedral : 3.797 54.444 3348 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.99 % Allowed : 8.85 % Favored : 90.16 % 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: 1.25 (0.15), residues: 3138 helix: 2.77 (0.18), residues: 855 sheet: 1.01 (0.20), residues: 678 loop : -0.33 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.020 0.001 TYR A1067 PHE 0.011 0.001 PHE D 238 TRP 0.025 0.002 TRP B 353 HIS 0.002 0.000 HIS D1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (23616) covalent geometry : angle 0.45652 / 0.24 (32361) SS BOND : bond 0.00203 / 0.11 ( 39) SS BOND : angle 0.45497 / 0.30 ( 78) hydrogen bonds : bond 0.03794 / 2.62 ( 1162) hydrogen bonds : angle 4.76564 / 3.36 ( 3297) link_BETA1-4 : bond 0.00354 / 0.21 ( 12) link_BETA1-4 : angle 0.71807 / 0.45 ( 36) link_NAG-ASN : bond 0.00292 / 0.17 ( 48) link_NAG-ASN : angle 1.40949 / 0.92 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6558 (m-80) cc_final: 0.6267 (m-80) REVERT: A 725 GLU cc_start: 0.8613 (tt0) cc_final: 0.8214 (tt0) REVERT: B 365 TYR cc_start: 0.8296 (m-80) cc_final: 0.7820 (m-80) REVERT: B 983 ARG cc_start: 0.8310 (mtm110) cc_final: 0.8084 (ttm170) REVERT: D 269 TYR cc_start: 0.8023 (m-10) cc_final: 0.7568 (m-10) REVERT: D 1002 GLN cc_start: 0.8385 (tp40) cc_final: 0.8148 (tp40) outliers start: 19 outliers final: 15 residues processed: 138 average time/residue: 0.1373 time to fit residues: 32.5483 Evaluate side-chains 125 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 35 optimal weight: 0.0020 chunk 185 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 40.0000 chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.133286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085617 restraints weight = 39298.441| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.63 r_work: 0.2980 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23715 Z= 0.106 Angle : 0.456 5.813 32619 Z= 0.236 Chirality : 0.043 0.172 4005 Planarity : 0.004 0.037 4182 Dihedral : 3.736 54.667 3348 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.15 % Allowed : 9.11 % Favored : 89.74 % 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: 1.28 (0.15), residues: 3138 helix: 2.80 (0.18), residues: 855 sheet: 1.00 (0.20), residues: 678 loop : -0.29 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.019 0.001 TYR B1067 PHE 0.011 0.001 PHE D 238 TRP 0.026 0.002 TRP B 353 HIS 0.002 0.000 HIS D1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (23616) covalent geometry : angle 0.44737 / 0.23 (32361) SS BOND : bond 0.00180 / 0.10 ( 39) SS BOND : angle 0.45962 / 0.30 ( 78) hydrogen bonds : bond 0.03629 / 2.52 ( 1162) hydrogen bonds : angle 4.68147 / 3.30 ( 3297) link_BETA1-4 : bond 0.00359 / 0.22 ( 12) link_BETA1-4 : angle 0.70393 / 0.45 ( 36) link_NAG-ASN : bond 0.00391 / 0.26 ( 48) link_NAG-ASN : angle 1.34398 / 0.88 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6528 (m-80) cc_final: 0.6241 (m-80) REVERT: A 725 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: A 858 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8759 (pp) REVERT: B 365 TYR cc_start: 0.8284 (m-80) cc_final: 0.7855 (m-80) REVERT: B 858 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8848 (pp) REVERT: B 1002 GLN cc_start: 0.8009 (tp40) cc_final: 0.7754 (tp40) REVERT: B 1094 VAL cc_start: 0.8860 (m) cc_final: 0.8514 (p) REVERT: D 41 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7804 (mtpp) REVERT: D 269 TYR cc_start: 0.7939 (m-10) cc_final: 0.7317 (m-10) REVERT: D 858 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8841 (pp) REVERT: D 1002 GLN cc_start: 0.8331 (tp40) cc_final: 0.8103 (tp40) outliers start: 22 outliers final: 15 residues processed: 139 average time/residue: 0.1338 time to fit residues: 32.4948 Evaluate side-chains 134 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 202 optimal weight: 0.6980 chunk 244 optimal weight: 0.0040 chunk 221 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN A1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.130266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082447 restraints weight = 39621.868| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.06 r_work: 0.2961 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23715 Z= 0.214 Angle : 0.529 6.596 32619 Z= 0.272 Chirality : 0.045 0.180 4005 Planarity : 0.004 0.035 4182 Dihedral : 4.005 54.733 3348 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.35 % Allowed : 9.17 % Favored : 89.48 % 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: 1.07 (0.15), residues: 3138 helix: 2.54 (0.18), residues: 873 sheet: 0.77 (0.20), residues: 699 loop : -0.36 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.021 0.001 TYR A1067 PHE 0.016 0.001 PHE A 92 TRP 0.033 0.002 TRP B 353 HIS 0.005 0.001 HIS D1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (23616) covalent geometry : angle 0.51954 / 0.27 (32361) SS BOND : bond 0.00371 / 0.20 ( 39) SS BOND : angle 0.55509 / 0.37 ( 78) hydrogen bonds : bond 0.04420 / 3.06 ( 1162) hydrogen bonds : angle 4.91676 / 3.48 ( 3297) link_BETA1-4 : bond 0.00292 / 0.15 ( 12) link_BETA1-4 : angle 0.72045 / 0.46 ( 36) link_NAG-ASN : bond 0.00314 / 0.19 ( 48) link_NAG-ASN : angle 1.58061 / 1.05 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6679 (m-80) cc_final: 0.6377 (m-80) REVERT: A 858 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8857 (pp) REVERT: B 365 TYR cc_start: 0.8321 (m-80) cc_final: 0.7846 (m-80) REVERT: B 858 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8933 (pp) REVERT: B 1002 GLN cc_start: 0.8364 (tp40) cc_final: 0.8125 (tp40) REVERT: D 41 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7832 (mtpp) REVERT: D 269 TYR cc_start: 0.7986 (m-10) cc_final: 0.7413 (m-10) REVERT: D 353 TRP cc_start: 0.8043 (p-90) cc_final: 0.7767 (p-90) REVERT: D 858 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8905 (pp) REVERT: D 1002 GLN cc_start: 0.8671 (tp40) cc_final: 0.8357 (tp40) outliers start: 26 outliers final: 18 residues processed: 141 average time/residue: 0.1350 time to fit residues: 33.0523 Evaluate side-chains 133 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 243 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 292 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.130523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082526 restraints weight = 39569.530| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.11 r_work: 0.2959 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 23715 Z= 0.174 Angle : 0.681 59.200 32619 Z= 0.381 Chirality : 0.045 0.252 4005 Planarity : 0.004 0.050 4182 Dihedral : 4.008 54.865 3348 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.25 % Allowed : 9.43 % Favored : 89.32 % Cbeta Deviations : 0.03 % 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: 1.06 (0.15), residues: 3138 helix: 2.53 (0.18), residues: 873 sheet: 0.76 (0.20), residues: 699 loop : -0.37 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 237 TYR 0.021 0.001 TYR A1067 PHE 0.016 0.001 PHE A 898 TRP 0.032 0.002 TRP B 353 HIS 0.003 0.001 HIS D1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (23616) covalent geometry : angle 0.67420 / 0.38 (32361) SS BOND : bond 0.00311 / 0.17 ( 39) SS BOND : angle 0.52765 / 0.35 ( 78) hydrogen bonds : bond 0.04335 / 3.00 ( 1162) hydrogen bonds : angle 4.91177 / 3.48 ( 3297) link_BETA1-4 : bond 0.00268 / 0.15 ( 12) link_BETA1-4 : angle 0.73114 / 0.47 ( 36) link_NAG-ASN : bond 0.00300 / 0.18 ( 48) link_NAG-ASN : angle 1.58875 / 1.05 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6666 (m-80) cc_final: 0.6364 (m-80) REVERT: A 858 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8825 (pp) REVERT: B 365 TYR cc_start: 0.8317 (m-80) cc_final: 0.7837 (m-80) REVERT: B 858 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8922 (pp) REVERT: B 1002 GLN cc_start: 0.8335 (tp40) cc_final: 0.8099 (tp40) REVERT: D 41 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7812 (mtpp) REVERT: D 269 TYR cc_start: 0.7974 (m-10) cc_final: 0.7397 (m-10) REVERT: D 353 TRP cc_start: 0.8033 (p-90) cc_final: 0.7780 (p-90) REVERT: D 858 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8895 (pp) REVERT: D 1002 GLN cc_start: 0.8648 (tp40) cc_final: 0.8335 (tp40) outliers start: 24 outliers final: 18 residues processed: 134 average time/residue: 0.1322 time to fit residues: 31.4107 Evaluate side-chains 133 residues out of total 2811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 907 ASN Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 73 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 41 optimal weight: 40.0000 chunk 63 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 160 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.130522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082509 restraints weight = 39594.166| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.12 r_work: 0.2959 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 23715 Z= 0.174 Angle : 0.681 59.200 32619 Z= 0.381 Chirality : 0.045 0.252 4005 Planarity : 0.004 0.050 4182 Dihedral : 4.008 54.865 3348 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.20 % Allowed : 9.48 % Favored : 89.32 % Cbeta Deviations : 0.03 % 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: 1.06 (0.15), residues: 3138 helix: 2.53 (0.18), residues: 873 sheet: 0.76 (0.20), residues: 699 loop : -0.37 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 237 TYR 0.021 0.001 TYR A1067 PHE 0.016 0.001 PHE A 898 TRP 0.032 0.002 TRP B 353 HIS 0.003 0.001 HIS D1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (23616) covalent geometry : angle 0.67423 / 0.38 (32361) SS BOND : bond 0.00311 / 0.17 ( 39) SS BOND : angle 0.52765 / 0.35 ( 78) hydrogen bonds : bond 0.04335 / 3.00 ( 1162) hydrogen bonds : angle 4.91177 / 3.48 ( 3297) link_BETA1-4 : bond 0.00268 / 0.15 ( 12) link_BETA1-4 : angle 0.73114 / 0.47 ( 36) link_NAG-ASN : bond 0.00300 / 0.18 ( 48) link_NAG-ASN : angle 1.58875 / 1.05 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6041.25 seconds wall clock time: 103 minutes 53.72 seconds (6233.72 seconds total)