Starting phenix.real_space_refine on Sat Jul 4 18:26:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tn9_26005/07_2026/7tn9_26005.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tn9_26005/07_2026/7tn9_26005.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/7tn9_26005/07_2026/7tn9_26005.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tn9_26005/07_2026/7tn9_26005.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tn9_26005/07_2026/7tn9_26005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tn9_26005/07_2026/7tn9_26005.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tn9_26005/07_2026/7tn9_26005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tn9_26005/07_2026/7tn9_26005.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= -0.000 sd= 0.030 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 97 5.16 5 C 14320 2.51 5 N 3791 2.21 5 O 4413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 222 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: 22621 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "T" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2127 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 13, 'TRANS': 255} Chain breaks: 1 Chain: "S" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1872 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 13, 'TRANS': 223} Chain breaks: 3 Chain: "U" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2127 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 13, 'TRANS': 255} Chain breaks: 2 Chain: "R" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "N" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 779 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "W" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 862 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "Q" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 878 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "M" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 869 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "G" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 912 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "H" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 760 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "O" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 869 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "V" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 862 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "X" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 839 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 899 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "J" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 728 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "D" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" 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: "U" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.30, per 1000 atoms: 0.23 Number of scatterers: 22621 At special positions: 0 Unit cell: (138.653, 155.459, 143.905, 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 97 16.00 O 4413 8.00 N 3791 7.00 C 14320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS T 108 " - pdb=" SG CYS T 135 " distance=2.02 Simple disulfide: pdb=" SG CYS T 121 " - pdb=" SG CYS T 147 " distance=2.03 Simple disulfide: pdb=" SG CYS S 53 " - pdb=" SG CYS V 609 " distance=2.03 Simple disulfide: pdb=" SG CYS S 108 " - pdb=" SG CYS S 135 " distance=2.03 Simple disulfide: pdb=" SG CYS S 121 " - pdb=" SG CYS S 147 " distance=2.02 Simple disulfide: pdb=" SG CYS U 53 " - pdb=" SG CYS X 609 " distance=2.02 Simple disulfide: pdb=" SG CYS U 108 " - pdb=" SG CYS U 135 " distance=2.02 Simple disulfide: pdb=" SG CYS U 121 " - pdb=" SG CYS U 147 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS W 511 " - pdb=" SG CYS W 556 " distance=2.03 Simple disulfide: pdb=" SG CYS W 601 " - pdb=" SG CYS W 608 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 511 " - pdb=" SG CYS V 556 " distance=2.03 Simple disulfide: pdb=" SG CYS V 601 " - pdb=" SG CYS V 608 " distance=2.03 Simple disulfide: pdb=" SG CYS X 511 " - pdb=" SG CYS X 556 " distance=2.03 Simple disulfide: pdb=" SG CYS X 601 " - pdb=" SG CYS X 608 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 94 " distance=2.03 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 ALPHA1-3 " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 6 " " BMA Y 3 " - " MAN Y 6 " ALPHA1-6 " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " NAG-ASN " NAG K 1 " - " ASN W 563 " " NAG L 1 " - " ASN V 563 " " NAG S 401 " - " ASN S 228 " " NAG S 402 " - " ASN S 238 " " NAG T 601 " - " ASN T 228 " " NAG T 602 " - " ASN T 238 " " NAG T 603 " - " ASN T 257 " " NAG U 601 " - " ASN U 228 " " NAG U 602 " - " ASN U 238 " " NAG U 603 " - " ASN U 257 " " NAG Y 1 " - " ASN X 563 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5190 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 54 sheets defined 11.1% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'T' and resid 71 through 74 removed outlier: 3.503A pdb=" N GLY T 74 " --> pdb=" O GLU T 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 71 through 74' Processing helix chain 'T' and resid 78 through 85 removed outlier: 3.737A pdb=" N LYS T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG T 85 " --> pdb=" O SER T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 264 Processing helix chain 'T' and resid 291 through 296 Processing helix chain 'S' and resid 59 through 61 No H-bonds generated for 'chain 'S' and resid 59 through 61' Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'S' and resid 78 through 85 removed outlier: 3.836A pdb=" N LYS S 84 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG S 85 " --> pdb=" O SER S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 196 removed outlier: 3.645A pdb=" N SER S 195 " --> pdb=" O LYS S 191 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER S 196 " --> pdb=" O ASP S 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 191 through 196' Processing helix chain 'S' and resid 249 through 261 removed outlier: 3.750A pdb=" N ASN S 257 " --> pdb=" O LEU S 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU S 258 " --> pdb=" O LEU S 254 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR S 261 " --> pdb=" O ASN S 257 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 74 Processing helix chain 'U' and resid 78 through 85 removed outlier: 3.625A pdb=" N LYS U 84 " --> pdb=" O PRO U 80 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG U 85 " --> pdb=" O SER U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 249 through 264 Processing helix chain 'U' and resid 289 through 296 removed outlier: 3.582A pdb=" N LYS U 295 " --> pdb=" O TRP U 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 84 removed outlier: 4.168A pdb=" N ALA N 84 " --> pdb=" O GLU N 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 538 through 541 Processing helix chain 'W' and resid 551 through 576 removed outlier: 3.956A pdb=" N ILE W 555 " --> pdb=" O GLN W 551 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN W 567 " --> pdb=" O ASN W 563 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA W 568 " --> pdb=" O GLU W 564 " (cutoff:3.500A) Processing helix chain 'W' and resid 583 through 597 Processing helix chain 'Q' and resid 87 through 91 Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.588A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'P' and resid 79 through 84 removed outlier: 3.691A pdb=" N ALA P 84 " --> pdb=" O GLU P 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'V' and resid 528 through 532 removed outlier: 3.605A pdb=" N TRP V 531 " --> pdb=" O GLY V 528 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE V 532 " --> pdb=" O LEU V 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 528 through 532' Processing helix chain 'V' and resid 538 through 542 removed outlier: 3.675A pdb=" N ILE V 542 " --> pdb=" O ALA V 539 " (cutoff:3.500A) Processing helix chain 'V' and resid 551 through 576 removed outlier: 3.784A pdb=" N ILE V 555 " --> pdb=" O GLN V 551 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN V 560 " --> pdb=" O CYS V 556 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN V 567 " --> pdb=" O ASN V 563 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA V 568 " --> pdb=" O GLU V 564 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU V 571 " --> pdb=" O GLN V 567 " (cutoff:3.500A) Processing helix chain 'V' and resid 583 through 597 Processing helix chain 'X' and resid 539 through 541 No H-bonds generated for 'chain 'X' and resid 539 through 541' Processing helix chain 'X' and resid 551 through 576 removed outlier: 3.587A pdb=" N ILE X 555 " --> pdb=" O GLN X 551 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN X 567 " --> pdb=" O ASN X 563 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA X 568 " --> pdb=" O GLU X 564 " (cutoff:3.500A) Processing helix chain 'X' and resid 583 through 597 Processing helix chain 'I' and resid 62 through 65 removed outlier: 4.018A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.975A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'D' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.600A pdb=" N SER A 77 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.020A pdb=" N GLY A 10 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.020A pdb=" N GLY A 10 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 107 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.974A pdb=" N GLY T 36 " --> pdb=" O ILE T 185 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASN T 69 " --> pdb=" O GLU T 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.974A pdb=" N GLY T 36 " --> pdb=" O ILE T 185 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL T 96 " --> pdb=" O THR W 581 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 86 through 89 Processing sheet with id=AA7, first strand: chain 'T' and resid 105 through 111 removed outlier: 6.272A pdb=" N GLU T 106 " --> pdb=" O TYR T 137 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS T 139 " --> pdb=" O GLU T 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS T 108 " --> pdb=" O HIS T 139 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL T 141 " --> pdb=" O CYS T 108 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN T 110 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY T 143 " --> pdb=" O ASN T 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG T 136 " --> pdb=" O THR T 216 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE T 218 " --> pdb=" O ARG T 136 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL T 138 " --> pdb=" O ILE T 218 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR T 220 " --> pdb=" O VAL T 138 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS T 140 " --> pdb=" O TYR T 220 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA T 222 " --> pdb=" O LYS T 140 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER T 142 " --> pdb=" O ALA T 222 " (cutoff:3.500A) removed outlier: 13.768A pdb=" N THR T 217 " --> pdb=" O ASP T 237 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N ASP T 237 " --> pdb=" O THR T 217 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG T 219 " --> pdb=" O GLU T 235 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR T 240 " --> pdb=" O VAL T 236 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL T 277 " --> pdb=" O GLN T 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 42 through 45 removed outlier: 6.844A pdb=" N GLY S 36 " --> pdb=" O ILE S 185 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA S 101 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER S 65 " --> pdb=" O ALA S 101 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLU S 103 " --> pdb=" O SER S 65 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLY S 67 " --> pdb=" O GLU S 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 42 through 45 removed outlier: 6.844A pdb=" N GLY S 36 " --> pdb=" O ILE S 185 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 96 " --> pdb=" O THR V 581 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 86 through 89 Processing sheet with id=AB2, first strand: chain 'S' and resid 105 through 114 removed outlier: 6.279A pdb=" N GLU S 106 " --> pdb=" O TYR S 137 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HIS S 139 " --> pdb=" O GLU S 106 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS S 108 " --> pdb=" O HIS S 139 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL S 141 " --> pdb=" O CYS S 108 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN S 110 " --> pdb=" O VAL S 141 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY S 143 " --> pdb=" O ASN S 110 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU S 112 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG S 219 " --> pdb=" O GLU S 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 42 through 45 removed outlier: 6.822A pdb=" N GLY U 36 " --> pdb=" O ILE U 185 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ALA U 101 " --> pdb=" O LEU U 63 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER U 65 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLU U 103 " --> pdb=" O SER U 65 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLY U 67 " --> pdb=" O GLU U 103 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU X 515 " --> pdb=" O MET X 548 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 42 through 45 removed outlier: 6.822A pdb=" N GLY U 36 " --> pdb=" O ILE U 185 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL U 96 " --> pdb=" O THR X 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'U' and resid 105 through 109 removed outlier: 6.244A pdb=" N GLU U 106 " --> pdb=" O TYR U 137 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS U 139 " --> pdb=" O GLU U 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS U 108 " --> pdb=" O HIS U 139 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL U 141 " --> pdb=" O CYS U 108 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY U 143 " --> pdb=" O GLU U 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 105 through 109 removed outlier: 6.244A pdb=" N GLU U 106 " --> pdb=" O TYR U 137 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS U 139 " --> pdb=" O GLU U 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS U 108 " --> pdb=" O HIS U 139 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL U 141 " --> pdb=" O CYS U 108 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG U 219 " --> pdb=" O GLU U 235 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL U 277 " --> pdb=" O GLN U 243 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE U 274 " --> pdb=" O VAL U 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AB9, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.707A pdb=" N LEU R 11 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.707A pdb=" N LEU R 11 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR R 96 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.663A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 45 through 46 Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.682A pdb=" N GLU F 76 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.667A pdb=" N GLU F 111 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.608A pdb=" N TYR F 31 " --> pdb=" O LYS F 36 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS F 36 " --> pdb=" O TYR F 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.272A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'M' and resid 58 through 60 removed outlier: 5.044A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.639A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.739A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 6 removed outlier: 5.925A pdb=" N THR H 69 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLN H 27 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N SER H 67 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N ILE H 29 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N SER H 65 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.903A pdb=" N LEU H 11 " --> pdb=" O LYS H 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 45 through 48 removed outlier: 6.414A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 4 through 6 removed outlier: 3.690A pdb=" N THR P 72 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 53 through 54 removed outlier: 5.530A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR P 85 " --> pdb=" O GLN P 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR P 96 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.858A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET O 34 " --> pdb=" O THR O 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.764A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP I 73 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.575A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.867A pdb=" N THR J 5 " --> pdb=" O ARG J 24 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.852A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'C' and resid 57 through 58 removed outlier: 3.786A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 57 through 58 removed outlier: 3.786A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.769A pdb=" N SER E 77 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.427A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.427A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.697A pdb=" N GLU B 76 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.790A pdb=" N ALA B 90 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 52 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.747A pdb=" N TYR B 31 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 36 " --> pdb=" O TYR B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.604A pdb=" N GLU D 76 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.749A pdb=" N LEU D 39 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR D 55 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP D 41 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.852A pdb=" N THR D 103 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.806A pdb=" N LYS D 36 " --> pdb=" O TYR D 31 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2007 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: 5.05 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7183 1.34 - 1.46: 6027 1.46 - 1.58: 9815 1.58 - 1.70: 1 1.70 - 1.82: 132 Bond restraints: 23158 Sorted by residual: bond pdb=" CG1 ILE V 527 " pdb=" CD1 ILE V 527 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.16e+00 bond pdb=" C1 MAN K 4 " pdb=" C2 MAN K 4 " ideal model delta sigma weight residual 1.526 1.583 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C5 MAN K 4 " pdb=" O5 MAN K 4 " ideal model delta sigma weight residual 1.418 1.466 -0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" CB CYS U 53 " pdb=" SG CYS U 53 " ideal model delta sigma weight residual 1.808 1.728 0.080 3.30e-02 9.18e+02 5.82e+00 bond pdb=" C ALA W 507 " pdb=" N GLN W 508 " ideal model delta sigma weight residual 1.329 1.291 0.038 1.60e-02 3.91e+03 5.66e+00 ... (remaining 23153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 31126 3.38 - 6.76: 290 6.76 - 10.14: 12 10.14 - 13.51: 6 13.51 - 16.89: 3 Bond angle restraints: 31437 Sorted by residual: angle pdb=" CB LYS I 76 " pdb=" CG LYS I 76 " pdb=" CD LYS I 76 " ideal model delta sigma weight residual 111.30 125.59 -14.29 2.30e+00 1.89e-01 3.86e+01 angle pdb=" C ALA W 507 " pdb=" N GLN W 508 " pdb=" CA GLN W 508 " ideal model delta sigma weight residual 120.49 127.60 -7.11 1.42e+00 4.96e-01 2.51e+01 angle pdb=" CA LEU T 51 " pdb=" CB LEU T 51 " pdb=" CG LEU T 51 " ideal model delta sigma weight residual 116.30 133.19 -16.89 3.50e+00 8.16e-02 2.33e+01 angle pdb=" CA CYS U 53 " pdb=" CB CYS U 53 " pdb=" SG CYS U 53 " ideal model delta sigma weight residual 114.40 125.23 -10.83 2.30e+00 1.89e-01 2.22e+01 angle pdb=" CA PRO V 606 " pdb=" N PRO V 606 " pdb=" CD PRO V 606 " ideal model delta sigma weight residual 112.00 105.43 6.57 1.40e+00 5.10e-01 2.20e+01 ... (remaining 31432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12295 17.94 - 35.87: 888 35.87 - 53.81: 155 53.81 - 71.74: 24 71.74 - 89.68: 16 Dihedral angle restraints: 13378 sinusoidal: 5193 harmonic: 8185 Sorted by residual: dihedral pdb=" CB CYS W 511 " pdb=" SG CYS W 511 " pdb=" SG CYS W 556 " pdb=" CB CYS W 556 " ideal model delta sinusoidal sigma weight residual 93.00 166.04 -73.04 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 94 " pdb=" CB CYS D 94 " ideal model delta sinusoidal sigma weight residual 93.00 158.56 -65.56 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS W 601 " pdb=" SG CYS W 601 " pdb=" SG CYS W 608 " pdb=" CB CYS W 608 " ideal model delta sinusoidal sigma weight residual -86.00 -25.48 -60.52 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 13375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 3476 0.164 - 0.329: 21 0.329 - 0.493: 2 0.493 - 0.658: 0 0.658 - 0.822: 1 Chirality restraints: 3500 Sorted by residual: chirality pdb=" C5 MAN K 4 " pdb=" C4 MAN K 4 " pdb=" C6 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False -2.51 -1.69 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C5 BMA Y 3 " pdb=" C4 BMA Y 3 " pdb=" C6 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.67 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA CYS U 53 " pdb=" N CYS U 53 " pdb=" C CYS U 53 " pdb=" CB CYS U 53 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 3497 not shown) Planarity restraints: 3997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY V 605 " -0.117 5.00e-02 4.00e+02 1.76e-01 4.93e+01 pdb=" N PRO V 606 " 0.303 5.00e-02 4.00e+02 pdb=" CA PRO V 606 " -0.100 5.00e-02 4.00e+02 pdb=" CD PRO V 606 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR M 101 " 0.087 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO M 102 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO M 102 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO M 102 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 68 " 0.022 2.00e-02 2.50e+03 2.31e-02 9.37e+00 pdb=" CG PHE G 68 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE G 68 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE G 68 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE G 68 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE G 68 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 68 " 0.001 2.00e-02 2.50e+03 ... (remaining 3994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 306 2.60 - 3.17: 20546 3.17 - 3.75: 35950 3.75 - 4.32: 52450 4.32 - 4.90: 86037 Nonbonded interactions: 195289 Sorted by model distance: nonbonded pdb=" OG SER N 63 " pdb=" OG1 THR N 74 " model vdw 2.024 3.040 nonbonded pdb=" NE1 TRP S 104 " pdb=" OE2 GLU V 545 " model vdw 2.059 3.120 nonbonded pdb=" NZ LYS B 24 " pdb=" OE1 GLU B 76 " model vdw 2.076 3.120 nonbonded pdb=" O SER H 63 " pdb=" OG1 THR H 74 " model vdw 2.104 3.040 nonbonded pdb=" NE2 GLN N 6 " pdb=" O GLN N 99 " model vdw 2.114 3.120 ... (remaining 195284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1 through 113) selection = chain 'I' } ncs_group { reference = (chain 'H' and (resid 2 through 10 or resid 22 through 30 or resid 33 or resid 3 \ 5 through 52 or resid 54 through 91 or resid 93 through 94 or resid 99 through 1 \ 03)) selection = (chain 'J' and (resid 2 through 30 or resid 33 or resid 35 through 52 or resid 5 \ 4 through 91 or resid 93 through 94 or resid 99 through 103)) selection = (chain 'N' and (resid 2 through 10 or resid 22 through 30 or resid 33 or resid 3 \ 5 through 52 or resid 54 through 91 or resid 93 through 94 or resid 97 through 1 \ 01)) selection = (chain 'P' and (resid 2 through 10 or resid 22 through 30 or resid 33 or resid 3 \ 5 through 52 or resid 54 through 91 or resid 93 through 94 or resid 97 through 1 \ 01)) selection = (chain 'R' and (resid 2 through 10 or resid 22 through 30 or resid 33 or resid 3 \ 5 through 52 or resid 54 through 91 or resid 93 through 94 or resid 97 through 1 \ 01)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'Y' } ncs_group { reference = chain 'M' selection = chain 'O' selection = (chain 'Q' and resid 2 through 116) } ncs_group { reference = chain 'S' selection = (chain 'T' and (resid 32 through 261 or resid 271 through 279 or resid 283 throu \ gh 292 or resid 602 through 603)) selection = (chain 'U' and (resid 32 through 261 or resid 271 through 279 or resid 283 throu \ gh 292 or resid 602 through 603)) } ncs_group { reference = (chain 'V' and resid 507 through 613) selection = (chain 'W' and resid 507 through 613) selection = chain 'X' } 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: 8.980 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.780 Find NCS groups from input model: 0.570 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 : 0.006 0.111 23214 Z= 0.277 Angle : 0.873 16.893 31575 Z= 0.460 Chirality : 0.054 0.822 3500 Planarity : 0.006 0.176 3986 Dihedral : 12.609 89.679 8098 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.46 (0.16), residues: 2817 helix: 1.41 (0.37), residues: 196 sheet: 0.85 (0.16), residues: 1008 loop : -0.15 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 72 TYR 0.033 0.002 TYR O 32 PHE 0.052 0.003 PHE G 68 TRP 0.048 0.002 TRP U 86 HIS 0.011 0.002 HIS O 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.28 (23158) covalent geometry : angle 0.85680 / 0.46 (31437) SS BOND : bond 0.00486 / 0.28 ( 30) SS BOND : angle 2.55095 / 1.75 ( 60) hydrogen bonds : bond 0.24278 / 16.55 ( 753) hydrogen bonds : angle 9.28917 / 6.55 ( 2007) link_ALPHA1-3 : bond 0.00159 / 0.08 ( 3) link_ALPHA1-3 : angle 3.17907 / 1.64 ( 9) link_ALPHA1-6 : bond 0.00807 / 0.50 ( 6) link_ALPHA1-6 : angle 2.65147 / 1.46 ( 18) link_BETA1-4 : bond 0.00538 / 0.32 ( 6) link_BETA1-4 : angle 2.17616 / 1.11 ( 18) link_NAG-ASN : bond 0.00531 / 0.40 ( 11) link_NAG-ASN : angle 3.09737 / 2.12 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8300 (tm-30) REVERT: A 79 TYR cc_start: 0.8381 (m-80) cc_final: 0.8123 (m-80) REVERT: S 251 GLN cc_start: 0.8113 (mp10) cc_final: 0.7672 (mp10) REVERT: R 42 LYS cc_start: 0.8521 (mppt) cc_final: 0.7984 (mppt) REVERT: R 79 GLN cc_start: 0.7668 (mp10) cc_final: 0.7196 (mp10) REVERT: R 87 TYR cc_start: 0.9317 (m-80) cc_final: 0.9041 (m-80) REVERT: R 105 ILE cc_start: 0.7980 (tp) cc_final: 0.7615 (tp) REVERT: N 75 ILE cc_start: 0.9131 (mp) cc_final: 0.8847 (mm) REVERT: N 89 GLN cc_start: 0.8636 (tt0) cc_final: 0.8046 (tt0) REVERT: N 90 GLN cc_start: 0.8467 (pp30) cc_final: 0.8004 (pp30) REVERT: F 4 MET cc_start: 0.8943 (mmm) cc_final: 0.8269 (mmm) REVERT: F 24 LYS cc_start: 0.9078 (ttpp) cc_final: 0.8768 (ttmm) REVERT: W 552 ASP cc_start: 0.8203 (t70) cc_final: 0.7884 (t0) REVERT: Q 3 GLN cc_start: 0.7958 (mm110) cc_final: 0.7754 (mm110) REVERT: Q 4 LEU cc_start: 0.9081 (mt) cc_final: 0.8708 (mt) REVERT: M 13 GLN cc_start: 0.8900 (mm110) cc_final: 0.8403 (mm-40) REVERT: M 18 LEU cc_start: 0.7362 (tp) cc_final: 0.7157 (tp) REVERT: M 27 PHE cc_start: 0.6221 (m-80) cc_final: 0.5989 (m-10) REVERT: M 60 TYR cc_start: 0.8064 (m-80) cc_final: 0.7351 (m-80) REVERT: M 73 ASP cc_start: 0.8168 (t0) cc_final: 0.7274 (t70) REVERT: M 76 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8620 (mmtm) REVERT: M 106 ASP cc_start: 0.7549 (p0) cc_final: 0.7263 (p0) REVERT: H 2 ILE cc_start: 0.7651 (mt) cc_final: 0.7432 (tp) REVERT: P 3 GLN cc_start: 0.7990 (mp10) cc_final: 0.7497 (mp10) REVERT: P 27 GLN cc_start: 0.7142 (mp10) cc_final: 0.6500 (mp10) REVERT: P 38 GLN cc_start: 0.8362 (tt0) cc_final: 0.7300 (tt0) REVERT: P 61 ARG cc_start: 0.8889 (ptp90) cc_final: 0.8542 (ptp90) REVERT: P 90 GLN cc_start: 0.8005 (pp30) cc_final: 0.7781 (pp30) REVERT: P 92 TYR cc_start: 0.9158 (t80) cc_final: 0.8708 (t80) REVERT: O 20 LEU cc_start: 0.8329 (mp) cc_final: 0.8036 (mt) REVERT: O 34 MET cc_start: 0.8775 (mmt) cc_final: 0.8275 (mmt) REVERT: O 39 GLN cc_start: 0.8424 (tt0) cc_final: 0.8016 (tt0) REVERT: O 50 THR cc_start: 0.8574 (m) cc_final: 0.8226 (m) REVERT: O 87 ARG cc_start: 0.7797 (mtm180) cc_final: 0.7412 (mtm180) REVERT: V 522 ASP cc_start: 0.7919 (m-30) cc_final: 0.7676 (t0) REVERT: V 578 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7353 (mm-30) REVERT: I 32 TYR cc_start: 0.7173 (m-80) cc_final: 0.6802 (m-10) REVERT: I 38 ARG cc_start: 0.6208 (ttp-110) cc_final: 0.5754 (ttm110) REVERT: I 53 HIS cc_start: 0.8803 (p-80) cc_final: 0.8562 (p-80) REVERT: I 57 ASP cc_start: 0.8507 (t0) cc_final: 0.8287 (t0) REVERT: I 81 LEU cc_start: 0.8630 (tp) cc_final: 0.8289 (tp) REVERT: I 99 ASN cc_start: 0.8737 (t0) cc_final: 0.8089 (t0) REVERT: J 45 LYS cc_start: 0.8460 (mptt) cc_final: 0.8209 (mmtt) REVERT: J 55 GLN cc_start: 0.8556 (tt0) cc_final: 0.8285 (tt0) REVERT: E 2 VAL cc_start: 0.9216 (t) cc_final: 0.8950 (t) REVERT: B 35 ASN cc_start: 0.9169 (t0) cc_final: 0.8944 (t0) REVERT: B 55 TYR cc_start: 0.9078 (p90) cc_final: 0.8643 (p90) REVERT: D 35 ASN cc_start: 0.9180 (t0) cc_final: 0.8905 (t0) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.1588 time to fit residues: 116.5720 Evaluate side-chains 383 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN T 278 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 221 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** W 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN P 55 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN V 521 GLN V 567 GLN X 551 GLN I 82 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078132 restraints weight = 66266.864| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.40 r_work: 0.2907 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 23214 Z= 0.188 Angle : 0.688 13.568 31575 Z= 0.360 Chirality : 0.047 0.333 3500 Planarity : 0.005 0.097 3986 Dihedral : 5.245 22.899 3124 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.62 % Allowed : 9.06 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2817 helix: 1.18 (0.40), residues: 196 sheet: 0.61 (0.16), residues: 1006 loop : -0.18 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 61 TYR 0.030 0.002 TYR T 162 PHE 0.023 0.002 PHE M 27 TRP 0.022 0.002 TRP U 86 HIS 0.008 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (23158) covalent geometry : angle 0.67699 / 0.36 (31437) SS BOND : bond 0.00384 / 0.25 ( 30) SS BOND : angle 1.10271 / 0.77 ( 60) hydrogen bonds : bond 0.04567 / 3.07 ( 753) hydrogen bonds : angle 6.72258 / 4.71 ( 2007) link_ALPHA1-3 : bond 0.00193 / 0.10 ( 3) link_ALPHA1-3 : angle 3.14405 / 1.64 ( 9) link_ALPHA1-6 : bond 0.00714 / 0.44 ( 6) link_ALPHA1-6 : angle 2.08180 / 1.23 ( 18) link_BETA1-4 : bond 0.00376 / 0.19 ( 6) link_BETA1-4 : angle 1.85538 / 1.04 ( 18) link_NAG-ASN : bond 0.00436 / 0.29 ( 11) link_NAG-ASN : angle 2.57438 / 1.79 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 431 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 79 TYR cc_start: 0.8689 (m-80) cc_final: 0.8347 (m-80) REVERT: T 78 ASP cc_start: 0.8073 (p0) cc_final: 0.7844 (p0) REVERT: T 127 ASP cc_start: 0.8879 (p0) cc_final: 0.8646 (p0) REVERT: S 251 GLN cc_start: 0.8286 (mp10) cc_final: 0.7911 (mp10) REVERT: U 221 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8562 (mm-40) REVERT: U 275 TRP cc_start: 0.8670 (m100) cc_final: 0.8460 (m100) REVERT: R 27 GLN cc_start: 0.8990 (pp30) cc_final: 0.8630 (pp30) REVERT: R 42 LYS cc_start: 0.8559 (mppt) cc_final: 0.7878 (mppt) REVERT: R 79 GLN cc_start: 0.7582 (mp10) cc_final: 0.7031 (mp10) REVERT: R 105 ILE cc_start: 0.8064 (tp) cc_final: 0.7648 (tp) REVERT: N 3 GLN cc_start: 0.7986 (mp10) cc_final: 0.7619 (mp10) REVERT: N 27 GLN cc_start: 0.7737 (mp10) cc_final: 0.7385 (mp10) REVERT: N 45 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8220 (ptmm) REVERT: N 61 ARG cc_start: 0.8433 (mtm110) cc_final: 0.7466 (ptp90) REVERT: N 79 GLN cc_start: 0.6925 (mp10) cc_final: 0.6389 (mp10) REVERT: N 89 GLN cc_start: 0.8433 (tt0) cc_final: 0.7927 (tt0) REVERT: F 11 LEU cc_start: 0.8886 (tp) cc_final: 0.8562 (tt) REVERT: F 17 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8138 (mt-10) REVERT: F 24 LYS cc_start: 0.9185 (ttpp) cc_final: 0.8751 (ttmm) REVERT: F 35 ASN cc_start: 0.9373 (t0) cc_final: 0.8991 (p0) REVERT: F 76 GLU cc_start: 0.7676 (pt0) cc_final: 0.7404 (pt0) REVERT: W 552 ASP cc_start: 0.8324 (t70) cc_final: 0.8006 (t0) REVERT: Q 3 GLN cc_start: 0.8220 (mm110) cc_final: 0.8007 (mm110) REVERT: Q 4 LEU cc_start: 0.9066 (mt) cc_final: 0.8693 (mt) REVERT: M 3 GLN cc_start: 0.7885 (mm110) cc_final: 0.7647 (mm110) REVERT: M 13 GLN cc_start: 0.8894 (mm110) cc_final: 0.8452 (mm-40) REVERT: M 27 PHE cc_start: 0.6244 (m-80) cc_final: 0.5835 (m-10) REVERT: M 50 THR cc_start: 0.8548 (t) cc_final: 0.8324 (t) REVERT: M 60 TYR cc_start: 0.8394 (m-80) cc_final: 0.7625 (m-80) REVERT: M 73 ASP cc_start: 0.7834 (t0) cc_final: 0.6980 (t0) REVERT: M 76 LYS cc_start: 0.9296 (mmtm) cc_final: 0.8932 (mmtm) REVERT: M 106 ASP cc_start: 0.7221 (p0) cc_final: 0.6965 (p0) REVERT: M 110 GLN cc_start: 0.8749 (tp40) cc_final: 0.8530 (mp10) REVERT: H 4 MET cc_start: 0.8107 (tpp) cc_final: 0.7269 (mmm) REVERT: H 23 CYS cc_start: 0.4516 (t) cc_final: 0.2419 (t) REVERT: H 27 GLN cc_start: 0.8329 (mt0) cc_final: 0.8108 (mp10) REVERT: P 3 GLN cc_start: 0.7926 (mp10) cc_final: 0.7427 (mp10) REVERT: P 4 MET cc_start: 0.6806 (mmm) cc_final: 0.5915 (mmm) REVERT: P 27 GLN cc_start: 0.6827 (mp10) cc_final: 0.6228 (mp10) REVERT: P 38 GLN cc_start: 0.8590 (tt0) cc_final: 0.8022 (tt0) REVERT: P 61 ARG cc_start: 0.8984 (ptp90) cc_final: 0.8489 (ptp90) REVERT: P 62 PHE cc_start: 0.8860 (m-80) cc_final: 0.8560 (m-80) REVERT: P 90 GLN cc_start: 0.8093 (pp30) cc_final: 0.7535 (pp30) REVERT: P 92 TYR cc_start: 0.9003 (t80) cc_final: 0.8765 (t80) REVERT: O 50 THR cc_start: 0.8704 (m) cc_final: 0.8375 (m) REVERT: O 84 ASN cc_start: 0.6821 (t0) cc_final: 0.6401 (t0) REVERT: O 90 ASP cc_start: 0.8446 (m-30) cc_final: 0.8225 (m-30) REVERT: V 522 ASP cc_start: 0.8304 (m-30) cc_final: 0.7730 (t0) REVERT: I 19 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7426 (ttp80) REVERT: I 32 TYR cc_start: 0.7252 (m-80) cc_final: 0.6848 (m-80) REVERT: I 53 HIS cc_start: 0.8579 (p-80) cc_final: 0.8343 (p-80) REVERT: I 57 ASP cc_start: 0.8625 (t0) cc_final: 0.8240 (t0) REVERT: I 80 TYR cc_start: 0.8666 (m-10) cc_final: 0.8396 (m-10) REVERT: I 81 LEU cc_start: 0.7588 (tp) cc_final: 0.7300 (tt) REVERT: I 99 ASN cc_start: 0.8242 (t0) cc_final: 0.7608 (t0) REVERT: I 105 TYR cc_start: 0.7247 (m-80) cc_final: 0.6975 (m-10) REVERT: J 45 LYS cc_start: 0.8431 (mptt) cc_final: 0.8185 (mmtt) REVERT: E 46 GLU cc_start: 0.8870 (tt0) cc_final: 0.8637 (pt0) REVERT: B 35 ASN cc_start: 0.9556 (t0) cc_final: 0.9212 (t0) REVERT: D 4 MET cc_start: 0.9117 (mmm) cc_final: 0.7733 (mmm) REVERT: D 35 ASN cc_start: 0.9549 (t0) cc_final: 0.9329 (t0) outliers start: 15 outliers final: 8 residues processed: 435 average time/residue: 0.1598 time to fit residues: 109.2175 Evaluate side-chains 393 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 385 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain E residue 3 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 263 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 62 GLN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 44 GLN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.102683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.076133 restraints weight = 66749.690| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.44 r_work: 0.2834 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23214 Z= 0.267 Angle : 0.674 11.797 31575 Z= 0.348 Chirality : 0.046 0.330 3500 Planarity : 0.004 0.071 3986 Dihedral : 5.228 22.766 3124 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.25 % Allowed : 11.26 % Favored : 87.49 % 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: -0.04 (0.15), residues: 2817 helix: 0.83 (0.39), residues: 204 sheet: 0.40 (0.16), residues: 966 loop : -0.35 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 72 TYR 0.028 0.002 TYR T 162 PHE 0.017 0.002 PHE S 234 TRP 0.019 0.002 TRP U 86 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 (23158) covalent geometry : angle 0.66353 / 0.35 (31437) SS BOND : bond 0.00381 / 0.25 ( 30) SS BOND : angle 0.92641 / 0.64 ( 60) hydrogen bonds : bond 0.04073 / 2.75 ( 753) hydrogen bonds : angle 6.14472 / 4.30 ( 2007) link_ALPHA1-3 : bond 0.00358 / 0.19 ( 3) link_ALPHA1-3 : angle 3.02682 / 1.58 ( 9) link_ALPHA1-6 : bond 0.00639 / 0.45 ( 6) link_ALPHA1-6 : angle 2.17571 / 1.25 ( 18) link_BETA1-4 : bond 0.00200 / 0.15 ( 6) link_BETA1-4 : angle 1.87559 / 1.03 ( 18) link_NAG-ASN : bond 0.00526 / 0.37 ( 11) link_NAG-ASN : angle 2.57277 / 1.81 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 407 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 79 TYR cc_start: 0.8790 (m-80) cc_final: 0.8539 (m-80) REVERT: T 127 ASP cc_start: 0.8879 (p0) cc_final: 0.8635 (p0) REVERT: S 251 GLN cc_start: 0.8401 (mp10) cc_final: 0.8080 (mp10) REVERT: U 221 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8476 (mm-40) REVERT: R 79 GLN cc_start: 0.7634 (mp10) cc_final: 0.7083 (mp10) REVERT: R 105 ILE cc_start: 0.7459 (tp) cc_final: 0.7147 (tp) REVERT: N 3 GLN cc_start: 0.8235 (mp10) cc_final: 0.7955 (mp10) REVERT: N 27 GLN cc_start: 0.7882 (mp10) cc_final: 0.7467 (mp10) REVERT: N 37 GLN cc_start: 0.8204 (tt0) cc_final: 0.7599 (tt0) REVERT: N 45 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8393 (ptmm) REVERT: N 61 ARG cc_start: 0.8474 (mtm110) cc_final: 0.7570 (ptp90) REVERT: N 75 ILE cc_start: 0.8979 (mp) cc_final: 0.8666 (mm) REVERT: N 79 GLN cc_start: 0.6968 (mp10) cc_final: 0.6421 (mp10) REVERT: N 89 GLN cc_start: 0.8642 (tt0) cc_final: 0.7878 (tt0) REVERT: F 9 ASP cc_start: 0.8989 (t0) cc_final: 0.8748 (t0) REVERT: F 24 LYS cc_start: 0.9204 (ttpp) cc_final: 0.8811 (ttmm) REVERT: W 552 ASP cc_start: 0.8376 (t70) cc_final: 0.8133 (t0) REVERT: W 564 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8663 (mt-10) REVERT: Q 46 GLU cc_start: 0.8743 (tt0) cc_final: 0.8530 (tt0) REVERT: M 3 GLN cc_start: 0.7816 (mm110) cc_final: 0.7538 (mm110) REVERT: M 13 GLN cc_start: 0.8937 (mm110) cc_final: 0.8492 (mm-40) REVERT: M 27 PHE cc_start: 0.6310 (m-80) cc_final: 0.5886 (m-10) REVERT: M 50 THR cc_start: 0.8613 (t) cc_final: 0.8319 (t) REVERT: M 73 ASP cc_start: 0.7713 (t0) cc_final: 0.6965 (t0) REVERT: M 76 LYS cc_start: 0.9275 (mmtm) cc_final: 0.8902 (mmtm) REVERT: M 110 GLN cc_start: 0.8731 (tp40) cc_final: 0.8455 (mp10) REVERT: G 65 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8576 (mmmm) REVERT: G 76 LYS cc_start: 0.9555 (mtpp) cc_final: 0.9243 (mttt) REVERT: G 83 MET cc_start: 0.9091 (mmm) cc_final: 0.8824 (mpp) REVERT: H 4 MET cc_start: 0.8303 (tpp) cc_final: 0.7834 (mmm) REVERT: H 23 CYS cc_start: 0.4786 (t) cc_final: 0.2388 (t) REVERT: P 3 GLN cc_start: 0.7874 (mp10) cc_final: 0.7401 (mp10) REVERT: P 27 GLN cc_start: 0.6967 (mp10) cc_final: 0.6231 (mp10) REVERT: P 38 GLN cc_start: 0.8573 (tt0) cc_final: 0.8336 (tt0) REVERT: P 61 ARG cc_start: 0.8935 (ptp90) cc_final: 0.8370 (ptp90) REVERT: P 62 PHE cc_start: 0.8939 (m-80) cc_final: 0.8619 (m-80) REVERT: P 90 GLN cc_start: 0.8248 (pp30) cc_final: 0.7927 (pp30) REVERT: P 92 TYR cc_start: 0.9021 (t80) cc_final: 0.8786 (t80) REVERT: O 34 MET cc_start: 0.8732 (mmp) cc_final: 0.8158 (mmp) REVERT: O 39 GLN cc_start: 0.7966 (tt0) cc_final: 0.7740 (tt0) REVERT: O 50 THR cc_start: 0.8856 (m) cc_final: 0.8512 (m) REVERT: O 84 ASN cc_start: 0.6812 (t0) cc_final: 0.6527 (t0) REVERT: V 522 ASP cc_start: 0.8253 (m-30) cc_final: 0.7724 (t0) REVERT: I 32 TYR cc_start: 0.7447 (m-80) cc_final: 0.7025 (m-80) REVERT: I 57 ASP cc_start: 0.8748 (t0) cc_final: 0.8387 (t0) REVERT: I 81 LEU cc_start: 0.7912 (tp) cc_final: 0.7427 (tt) REVERT: I 83 MET cc_start: 0.8681 (mtm) cc_final: 0.7970 (mpp) REVERT: I 99 ASN cc_start: 0.8321 (t0) cc_final: 0.7613 (t0) REVERT: J 45 LYS cc_start: 0.8458 (mptt) cc_final: 0.8176 (mmtt) REVERT: J 87 TYR cc_start: 0.6805 (m-80) cc_final: 0.6340 (m-80) REVERT: B 35 ASN cc_start: 0.9572 (t0) cc_final: 0.9243 (t0) REVERT: D 4 MET cc_start: 0.9126 (mmm) cc_final: 0.7747 (mmm) REVERT: D 76 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7844 (tm-30) outliers start: 30 outliers final: 22 residues processed: 423 average time/residue: 0.1516 time to fit residues: 101.2490 Evaluate side-chains 405 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 383 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain X residue 552 ASP Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 143 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 262 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 107 ASN U 255 GLN N 6 GLN F 27 GLN F 35 ASN W 508 GLN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 560 GLN J 37 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.105067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.078620 restraints weight = 65510.575| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.32 r_work: 0.2892 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23214 Z= 0.175 Angle : 0.622 11.244 31575 Z= 0.320 Chirality : 0.044 0.314 3500 Planarity : 0.004 0.060 3986 Dihedral : 5.019 20.829 3124 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.83 % Allowed : 12.30 % Favored : 85.87 % 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: -0.18 (0.15), residues: 2817 helix: 0.95 (0.39), residues: 198 sheet: 0.20 (0.16), residues: 983 loop : -0.40 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 18 TYR 0.026 0.001 TYR T 162 PHE 0.014 0.001 PHE M 27 TRP 0.014 0.001 TRP U 288 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (23158) covalent geometry : angle 0.61318 / 0.32 (31437) SS BOND : bond 0.00283 / 0.19 ( 30) SS BOND : angle 0.79762 / 0.56 ( 60) hydrogen bonds : bond 0.03520 / 2.38 ( 753) hydrogen bonds : angle 5.79734 / 4.06 ( 2007) link_ALPHA1-3 : bond 0.00307 / 0.16 ( 3) link_ALPHA1-3 : angle 2.83169 / 1.47 ( 9) link_ALPHA1-6 : bond 0.00760 / 0.54 ( 6) link_ALPHA1-6 : angle 2.01890 / 1.15 ( 18) link_BETA1-4 : bond 0.00128 / 0.06 ( 6) link_BETA1-4 : angle 1.75143 / 0.97 ( 18) link_NAG-ASN : bond 0.00417 / 0.28 ( 11) link_NAG-ASN : angle 2.31103 / 1.62 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 412 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8034 (tm-30) REVERT: T 127 ASP cc_start: 0.8839 (p0) cc_final: 0.8593 (p0) REVERT: S 251 GLN cc_start: 0.8390 (mp10) cc_final: 0.8028 (mp10) REVERT: U 221 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8357 (mm-40) REVERT: R 4 MET cc_start: 0.8562 (mmp) cc_final: 0.7882 (mmp) REVERT: R 79 GLN cc_start: 0.7638 (mp10) cc_final: 0.7183 (mp10) REVERT: R 105 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7231 (tp) REVERT: N 3 GLN cc_start: 0.8353 (mp10) cc_final: 0.8028 (mp10) REVERT: N 27 GLN cc_start: 0.7926 (mp10) cc_final: 0.7533 (mp10) REVERT: N 37 GLN cc_start: 0.8067 (tt0) cc_final: 0.7504 (tt0) REVERT: N 45 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8431 (ptmm) REVERT: N 61 ARG cc_start: 0.8490 (mtm110) cc_final: 0.7557 (ptp90) REVERT: N 79 GLN cc_start: 0.6848 (mp10) cc_final: 0.6078 (mp10) REVERT: N 82 ASP cc_start: 0.8174 (m-30) cc_final: 0.7510 (m-30) REVERT: N 89 GLN cc_start: 0.8573 (tt0) cc_final: 0.7999 (tt0) REVERT: F 9 ASP cc_start: 0.8948 (t0) cc_final: 0.8741 (t0) REVERT: F 17 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8194 (mt-10) REVERT: F 24 LYS cc_start: 0.9188 (ttpp) cc_final: 0.8878 (ttmm) REVERT: W 552 ASP cc_start: 0.8355 (t70) cc_final: 0.8147 (t0) REVERT: Q 32 TYR cc_start: 0.8176 (m-80) cc_final: 0.7629 (m-80) REVERT: Q 87 ARG cc_start: 0.7892 (ptp90) cc_final: 0.7588 (ptp90) REVERT: Q 89 GLU cc_start: 0.9186 (pm20) cc_final: 0.8953 (pm20) REVERT: Q 110 GLN cc_start: 0.8846 (tp-100) cc_final: 0.7861 (pp30) REVERT: M 13 GLN cc_start: 0.8927 (mm110) cc_final: 0.8468 (mm-40) REVERT: M 27 PHE cc_start: 0.6256 (m-80) cc_final: 0.6026 (m-10) REVERT: M 50 THR cc_start: 0.8672 (t) cc_final: 0.8436 (t) REVERT: M 110 GLN cc_start: 0.8781 (tp40) cc_final: 0.8560 (mp10) REVERT: G 65 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8592 (mmmm) REVERT: G 68 PHE cc_start: 0.8203 (m-10) cc_final: 0.7942 (m-10) REVERT: G 76 LYS cc_start: 0.9546 (mtpp) cc_final: 0.9297 (mttt) REVERT: G 83 MET cc_start: 0.8954 (mmm) cc_final: 0.8719 (mmm) REVERT: H 4 MET cc_start: 0.8361 (tpp) cc_final: 0.7938 (mmm) REVERT: H 23 CYS cc_start: 0.4621 (t) cc_final: 0.2428 (t) REVERT: H 27 GLN cc_start: 0.8355 (mt0) cc_final: 0.8013 (mp10) REVERT: P 3 GLN cc_start: 0.7848 (mp10) cc_final: 0.7488 (mp10) REVERT: P 38 GLN cc_start: 0.8499 (tt0) cc_final: 0.8084 (tt0) REVERT: P 61 ARG cc_start: 0.8912 (ptp90) cc_final: 0.8354 (ptp90) REVERT: P 62 PHE cc_start: 0.8953 (m-80) cc_final: 0.8635 (m-80) REVERT: P 90 GLN cc_start: 0.8297 (pp30) cc_final: 0.7927 (pp30) REVERT: P 92 TYR cc_start: 0.8954 (t80) cc_final: 0.8692 (t80) REVERT: O 34 MET cc_start: 0.8690 (mmt) cc_final: 0.8055 (mmp) REVERT: O 39 GLN cc_start: 0.8069 (tt0) cc_final: 0.7837 (tt0) REVERT: O 50 THR cc_start: 0.8826 (m) cc_final: 0.8524 (m) REVERT: O 76 LYS cc_start: 0.9311 (mptt) cc_final: 0.9107 (mmtm) REVERT: O 84 ASN cc_start: 0.6847 (t0) cc_final: 0.6603 (t0) REVERT: V 527 ILE cc_start: 0.7978 (mm) cc_final: 0.7764 (mm) REVERT: I 32 TYR cc_start: 0.7239 (m-80) cc_final: 0.6733 (m-80) REVERT: I 57 ASP cc_start: 0.8503 (t0) cc_final: 0.8181 (t0) REVERT: I 99 ASN cc_start: 0.8150 (t0) cc_final: 0.7402 (t0) REVERT: I 105 TYR cc_start: 0.7141 (m-10) cc_final: 0.6902 (m-10) REVERT: J 45 LYS cc_start: 0.8391 (mptt) cc_final: 0.8170 (mmtt) REVERT: J 48 ILE cc_start: 0.7703 (mp) cc_final: 0.7418 (tt) REVERT: J 87 TYR cc_start: 0.6941 (m-80) cc_final: 0.6457 (m-80) REVERT: E 58 TYR cc_start: 0.8699 (m-80) cc_final: 0.8487 (m-80) REVERT: B 35 ASN cc_start: 0.9524 (t0) cc_final: 0.9162 (t0) REVERT: D 4 MET cc_start: 0.9164 (mmm) cc_final: 0.7672 (mmm) outliers start: 44 outliers final: 29 residues processed: 433 average time/residue: 0.1603 time to fit residues: 109.5096 Evaluate side-chains 416 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 386 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 5 optimal weight: 0.1980 chunk 233 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 GLN R 3 GLN F 27 GLN F 35 ASN W 508 GLN W 595 GLN M 3 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.092904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.065371 restraints weight = 57056.378| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.70 r_work: 0.2891 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23214 Z= 0.147 Angle : 0.615 12.488 31575 Z= 0.314 Chirality : 0.044 0.311 3500 Planarity : 0.004 0.055 3986 Dihedral : 4.856 19.824 3124 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.41 % Allowed : 13.55 % Favored : 84.04 % 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: -0.26 (0.15), residues: 2817 helix: 0.95 (0.39), residues: 198 sheet: 0.05 (0.16), residues: 1012 loop : -0.39 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 18 TYR 0.025 0.001 TYR T 162 PHE 0.023 0.001 PHE S 234 TRP 0.015 0.001 TRP U 288 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (23158) covalent geometry : angle 0.60605 / 0.31 (31437) SS BOND : bond 0.00245 / 0.16 ( 30) SS BOND : angle 0.71801 / 0.49 ( 60) hydrogen bonds : bond 0.03331 / 2.25 ( 753) hydrogen bonds : angle 5.60095 / 3.93 ( 2007) link_ALPHA1-3 : bond 0.00296 / 0.15 ( 3) link_ALPHA1-3 : angle 2.74911 / 1.43 ( 9) link_ALPHA1-6 : bond 0.00668 / 0.48 ( 6) link_ALPHA1-6 : angle 1.90306 / 1.09 ( 18) link_BETA1-4 : bond 0.00158 / 0.06 ( 6) link_BETA1-4 : angle 1.68766 / 0.94 ( 18) link_NAG-ASN : bond 0.00388 / 0.24 ( 11) link_NAG-ASN : angle 2.22225 / 1.56 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 411 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8578 (tm-30) cc_final: 0.7911 (tm-30) REVERT: T 127 ASP cc_start: 0.8927 (p0) cc_final: 0.8661 (p0) REVERT: S 51 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8284 (tt) REVERT: S 251 GLN cc_start: 0.8333 (mp10) cc_final: 0.7976 (mp10) REVERT: R 3 GLN cc_start: 0.8460 (mm110) cc_final: 0.8250 (mm-40) REVERT: R 4 MET cc_start: 0.8516 (mmp) cc_final: 0.7959 (mmp) REVERT: R 24 ARG cc_start: 0.8858 (mtp-110) cc_final: 0.8614 (mtp-110) REVERT: R 79 GLN cc_start: 0.7597 (mp10) cc_final: 0.7155 (mp10) REVERT: R 105 ILE cc_start: 0.7704 (tp) cc_final: 0.7415 (tp) REVERT: N 3 GLN cc_start: 0.8267 (mp10) cc_final: 0.7939 (mp10) REVERT: N 27 GLN cc_start: 0.7907 (mp10) cc_final: 0.7513 (mp10) REVERT: N 45 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8389 (ptmm) REVERT: N 61 ARG cc_start: 0.8537 (mtm110) cc_final: 0.7592 (ptp90) REVERT: N 75 ILE cc_start: 0.8869 (mp) cc_final: 0.8605 (mm) REVERT: N 79 GLN cc_start: 0.6910 (mp10) cc_final: 0.6263 (mp10) REVERT: N 82 ASP cc_start: 0.8158 (m-30) cc_final: 0.7536 (m-30) REVERT: N 89 GLN cc_start: 0.8459 (tt0) cc_final: 0.7936 (tt0) REVERT: N 90 GLN cc_start: 0.8609 (pp30) cc_final: 0.8161 (pp30) REVERT: F 11 LEU cc_start: 0.8751 (tp) cc_final: 0.8544 (tp) REVERT: F 24 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8790 (ttmm) REVERT: W 508 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6657 (tt0) REVERT: W 548 MET cc_start: 0.8955 (mtm) cc_final: 0.8705 (mtp) REVERT: W 552 ASP cc_start: 0.8400 (t70) cc_final: 0.8200 (t0) REVERT: W 564 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8765 (mm-30) REVERT: Q 32 TYR cc_start: 0.8107 (m-80) cc_final: 0.7558 (m-80) REVERT: Q 87 ARG cc_start: 0.7897 (ptp90) cc_final: 0.7590 (ptp90) REVERT: Q 89 GLU cc_start: 0.9202 (pm20) cc_final: 0.8973 (pm20) REVERT: M 3 GLN cc_start: 0.7951 (mm110) cc_final: 0.7737 (mm110) REVERT: M 13 GLN cc_start: 0.8894 (mm110) cc_final: 0.8411 (mm-40) REVERT: M 27 PHE cc_start: 0.6242 (m-80) cc_final: 0.6007 (m-10) REVERT: M 50 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8385 (t) REVERT: G 65 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8495 (mmmm) REVERT: G 68 PHE cc_start: 0.8083 (m-10) cc_final: 0.7790 (m-10) REVERT: G 76 LYS cc_start: 0.9543 (mtpp) cc_final: 0.9286 (mttt) REVERT: G 80 TYR cc_start: 0.8535 (m-80) cc_final: 0.8121 (m-80) REVERT: G 83 MET cc_start: 0.8858 (mmm) cc_final: 0.8556 (mmm) REVERT: H 4 MET cc_start: 0.8323 (tpp) cc_final: 0.7869 (mmm) REVERT: H 23 CYS cc_start: 0.4809 (t) cc_final: 0.2583 (t) REVERT: H 27 GLN cc_start: 0.8417 (mt0) cc_final: 0.8042 (mp10) REVERT: H 32 TYR cc_start: 0.8472 (m-10) cc_final: 0.8154 (m-10) REVERT: P 3 GLN cc_start: 0.7793 (mp10) cc_final: 0.7419 (mp10) REVERT: P 38 GLN cc_start: 0.8546 (tt0) cc_final: 0.7956 (tt0) REVERT: P 61 ARG cc_start: 0.8887 (ptp90) cc_final: 0.8373 (ptp90) REVERT: P 62 PHE cc_start: 0.8936 (m-80) cc_final: 0.8625 (m-80) REVERT: P 90 GLN cc_start: 0.8197 (pp30) cc_final: 0.7749 (pp30) REVERT: P 92 TYR cc_start: 0.8844 (t80) cc_final: 0.8586 (t80) REVERT: O 34 MET cc_start: 0.8670 (mmt) cc_final: 0.8024 (mmp) REVERT: O 50 THR cc_start: 0.8720 (m) cc_final: 0.8449 (m) REVERT: O 74 ASN cc_start: 0.8099 (p0) cc_final: 0.7445 (m-40) REVERT: O 76 LYS cc_start: 0.9326 (mptt) cc_final: 0.9121 (mmtm) REVERT: O 84 ASN cc_start: 0.6817 (t0) cc_final: 0.6593 (t0) REVERT: V 527 ILE cc_start: 0.8034 (mm) cc_final: 0.7828 (mm) REVERT: V 540 GLU cc_start: 0.8869 (mp0) cc_final: 0.8609 (pm20) REVERT: X 560 GLN cc_start: 0.9112 (tp40) cc_final: 0.8899 (tp40) REVERT: I 19 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8228 (ttp80) REVERT: I 25 SER cc_start: 0.7849 (t) cc_final: 0.7499 (p) REVERT: I 32 TYR cc_start: 0.7210 (m-80) cc_final: 0.6658 (m-80) REVERT: I 53 HIS cc_start: 0.8729 (p90) cc_final: 0.8428 (p90) REVERT: I 57 ASP cc_start: 0.8428 (t0) cc_final: 0.8093 (t0) REVERT: I 83 MET cc_start: 0.8734 (mtm) cc_final: 0.8532 (mpp) REVERT: I 99 ASN cc_start: 0.8138 (t0) cc_final: 0.7357 (t0) REVERT: J 45 LYS cc_start: 0.8428 (mptt) cc_final: 0.8201 (mmtt) REVERT: J 48 ILE cc_start: 0.7701 (mp) cc_final: 0.7444 (tt) REVERT: J 87 TYR cc_start: 0.7038 (m-80) cc_final: 0.6534 (m-80) REVERT: E 58 TYR cc_start: 0.8686 (m-80) cc_final: 0.8429 (m-80) REVERT: B 35 ASN cc_start: 0.9606 (t0) cc_final: 0.9262 (t0) REVERT: D 4 MET cc_start: 0.9202 (mmm) cc_final: 0.7744 (mmm) outliers start: 58 outliers final: 38 residues processed: 447 average time/residue: 0.1515 time to fit residues: 107.5040 Evaluate side-chains 429 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 388 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain W residue 508 GLN Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain V residue 610 ILE Chi-restraints excluded: chain X residue 581 THR Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 125 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 107 ASN ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** W 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 GLN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.070973 restraints weight = 65894.264| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.56 r_work: 0.2813 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 23214 Z= 0.267 Angle : 0.657 16.171 31575 Z= 0.336 Chirality : 0.045 0.309 3500 Planarity : 0.004 0.051 3986 Dihedral : 4.963 21.754 3124 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.45 % Allowed : 14.34 % Favored : 83.21 % 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: -0.34 (0.16), residues: 2817 helix: 0.93 (0.39), residues: 204 sheet: -0.03 (0.16), residues: 999 loop : -0.43 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 18 TYR 0.026 0.002 TYR T 162 PHE 0.022 0.002 PHE S 234 TRP 0.016 0.001 TRP U 288 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.27 (23158) covalent geometry : angle 0.64795 / 0.33 (31437) SS BOND : bond 0.00366 / 0.24 ( 30) SS BOND : angle 0.84285 / 0.58 ( 60) hydrogen bonds : bond 0.03545 / 2.40 ( 753) hydrogen bonds : angle 5.59404 / 3.91 ( 2007) link_ALPHA1-3 : bond 0.00310 / 0.16 ( 3) link_ALPHA1-3 : angle 2.88266 / 1.50 ( 9) link_ALPHA1-6 : bond 0.00552 / 0.36 ( 6) link_ALPHA1-6 : angle 2.05387 / 1.19 ( 18) link_BETA1-4 : bond 0.00174 / 0.13 ( 6) link_BETA1-4 : angle 1.82648 / 1.01 ( 18) link_NAG-ASN : bond 0.00505 / 0.35 ( 11) link_NAG-ASN : angle 2.39951 / 1.69 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 395 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8605 (tm-30) cc_final: 0.7908 (tm-30) REVERT: T 127 ASP cc_start: 0.9029 (p0) cc_final: 0.8745 (p0) REVERT: S 51 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8253 (tt) REVERT: S 251 GLN cc_start: 0.8305 (mp10) cc_final: 0.7973 (mp10) REVERT: U 221 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8244 (mm-40) REVERT: R 4 MET cc_start: 0.8555 (mmp) cc_final: 0.8139 (mmp) REVERT: R 24 ARG cc_start: 0.8814 (mtp-110) cc_final: 0.8562 (mtp-110) REVERT: R 79 GLN cc_start: 0.7606 (mp10) cc_final: 0.7126 (mp10) REVERT: R 105 ILE cc_start: 0.7881 (tp) cc_final: 0.7611 (tp) REVERT: N 3 GLN cc_start: 0.8381 (mp10) cc_final: 0.7982 (mp10) REVERT: N 27 GLN cc_start: 0.7913 (mp10) cc_final: 0.7414 (mp10) REVERT: N 45 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8266 (ptmm) REVERT: N 61 ARG cc_start: 0.8485 (mtm110) cc_final: 0.7468 (ptp90) REVERT: N 75 ILE cc_start: 0.8828 (mp) cc_final: 0.8513 (mm) REVERT: N 79 GLN cc_start: 0.6935 (mp10) cc_final: 0.6375 (mp10) REVERT: N 82 ASP cc_start: 0.8121 (m-30) cc_final: 0.7489 (m-30) REVERT: N 89 GLN cc_start: 0.8464 (tt0) cc_final: 0.7737 (tt0) REVERT: N 90 GLN cc_start: 0.8661 (pp30) cc_final: 0.8019 (pp30) REVERT: F 17 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8185 (mt-10) REVERT: F 24 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8763 (ttmm) REVERT: F 35 ASN cc_start: 0.9574 (t0) cc_final: 0.9078 (t0) REVERT: F 61 GLU cc_start: 0.8639 (tp30) cc_final: 0.8307 (tp30) REVERT: W 548 MET cc_start: 0.9045 (mtm) cc_final: 0.8793 (mtp) REVERT: W 552 ASP cc_start: 0.8505 (t70) cc_final: 0.8290 (t0) REVERT: M 13 GLN cc_start: 0.8917 (mm110) cc_final: 0.8440 (mm-40) REVERT: M 27 PHE cc_start: 0.6303 (m-80) cc_final: 0.6016 (m-10) REVERT: M 87 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7546 (mtt90) REVERT: G 65 LYS cc_start: 0.8787 (mmmm) cc_final: 0.8476 (mmmm) REVERT: G 76 LYS cc_start: 0.9548 (mtpp) cc_final: 0.9275 (mttt) REVERT: H 4 MET cc_start: 0.8312 (tpp) cc_final: 0.7937 (mmm) REVERT: H 17 ASP cc_start: 0.6943 (t0) cc_final: 0.6681 (t0) REVERT: H 23 CYS cc_start: 0.4800 (t) cc_final: 0.2549 (t) REVERT: H 27 GLN cc_start: 0.8434 (mt0) cc_final: 0.8027 (mp10) REVERT: P 3 GLN cc_start: 0.7724 (mp10) cc_final: 0.7354 (mp10) REVERT: P 38 GLN cc_start: 0.8401 (tt0) cc_final: 0.8189 (tt0) REVERT: P 61 ARG cc_start: 0.8795 (ptp90) cc_final: 0.8241 (ptp90) REVERT: P 62 PHE cc_start: 0.9006 (m-80) cc_final: 0.8650 (m-80) REVERT: P 90 GLN cc_start: 0.8325 (pp30) cc_final: 0.7866 (pp30) REVERT: O 34 MET cc_start: 0.8550 (mmt) cc_final: 0.7876 (mmp) REVERT: O 39 GLN cc_start: 0.8001 (tt0) cc_final: 0.7795 (tt0) REVERT: O 50 THR cc_start: 0.8724 (m) cc_final: 0.8480 (m) REVERT: O 74 ASN cc_start: 0.8112 (p0) cc_final: 0.7469 (m-40) REVERT: V 540 GLU cc_start: 0.8938 (mp0) cc_final: 0.8608 (pm20) REVERT: X 567 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8299 (tp40) REVERT: I 19 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8032 (ttp80) REVERT: I 25 SER cc_start: 0.7813 (t) cc_final: 0.7477 (p) REVERT: I 32 TYR cc_start: 0.7252 (m-80) cc_final: 0.6707 (m-80) REVERT: I 53 HIS cc_start: 0.8622 (p90) cc_final: 0.8338 (p90) REVERT: I 57 ASP cc_start: 0.8490 (t0) cc_final: 0.8144 (t0) REVERT: I 99 ASN cc_start: 0.8075 (t0) cc_final: 0.7323 (t0) REVERT: J 45 LYS cc_start: 0.8343 (mptt) cc_final: 0.8137 (mmtt) REVERT: J 48 ILE cc_start: 0.7690 (mp) cc_final: 0.7408 (tt) REVERT: J 87 TYR cc_start: 0.7100 (m-80) cc_final: 0.6669 (m-80) REVERT: E 58 TYR cc_start: 0.8799 (m-80) cc_final: 0.8464 (m-80) REVERT: B 24 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8464 (ttmm) REVERT: B 35 ASN cc_start: 0.9656 (t0) cc_final: 0.9298 (t0) outliers start: 59 outliers final: 46 residues processed: 427 average time/residue: 0.1584 time to fit residues: 106.5346 Evaluate side-chains 422 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 374 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain V residue 610 ILE Chi-restraints excluded: chain X residue 567 GLN Chi-restraints excluded: chain X residue 581 THR Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 203 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 178 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN W 595 GLN M 3 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.084438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058722 restraints weight = 66750.198| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.50 r_work: 0.2828 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23214 Z= 0.207 Angle : 0.662 15.647 31575 Z= 0.337 Chirality : 0.045 0.306 3500 Planarity : 0.004 0.050 3986 Dihedral : 4.964 21.002 3124 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.41 % Allowed : 15.25 % Favored : 82.34 % 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: -0.40 (0.15), residues: 2817 helix: 0.88 (0.39), residues: 200 sheet: -0.07 (0.16), residues: 979 loop : -0.48 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 18 TYR 0.026 0.002 TYR T 162 PHE 0.022 0.001 PHE S 234 TRP 0.019 0.001 TRP U 288 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (23158) covalent geometry : angle 0.64617 / 0.33 (31437) SS BOND : bond 0.00314 / 0.21 ( 30) SS BOND : angle 2.35460 / 1.36 ( 60) hydrogen bonds : bond 0.03435 / 2.33 ( 753) hydrogen bonds : angle 5.58978 / 3.91 ( 2007) link_ALPHA1-3 : bond 0.00279 / 0.14 ( 3) link_ALPHA1-3 : angle 2.79053 / 1.45 ( 9) link_ALPHA1-6 : bond 0.00618 / 0.45 ( 6) link_ALPHA1-6 : angle 1.94979 / 1.12 ( 18) link_BETA1-4 : bond 0.00111 / 0.08 ( 6) link_BETA1-4 : angle 1.77881 / 0.99 ( 18) link_NAG-ASN : bond 0.00419 / 0.29 ( 11) link_NAG-ASN : angle 2.26577 / 1.58 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 391 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8596 (tm-30) cc_final: 0.7920 (tm-30) REVERT: T 127 ASP cc_start: 0.8981 (p0) cc_final: 0.8708 (p0) REVERT: S 51 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8207 (tt) REVERT: S 251 GLN cc_start: 0.8298 (mp10) cc_final: 0.7929 (mp10) REVERT: U 221 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8162 (mm-40) REVERT: R 4 MET cc_start: 0.8525 (mmp) cc_final: 0.8141 (mmp) REVERT: R 24 ARG cc_start: 0.8851 (mtp-110) cc_final: 0.8587 (mtp-110) REVERT: R 79 GLN cc_start: 0.7662 (mp10) cc_final: 0.7149 (mp10) REVERT: R 105 ILE cc_start: 0.7669 (tp) cc_final: 0.7381 (tp) REVERT: N 3 GLN cc_start: 0.8377 (mp10) cc_final: 0.7909 (mp10) REVERT: N 27 GLN cc_start: 0.7942 (mp10) cc_final: 0.7372 (mp10) REVERT: N 37 GLN cc_start: 0.7644 (tt0) cc_final: 0.6794 (tt0) REVERT: N 45 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8310 (ptmm) REVERT: N 61 ARG cc_start: 0.8491 (mtm110) cc_final: 0.7572 (ptp90) REVERT: N 75 ILE cc_start: 0.8837 (mp) cc_final: 0.8534 (mm) REVERT: N 82 ASP cc_start: 0.8084 (m-30) cc_final: 0.7415 (m-30) REVERT: N 89 GLN cc_start: 0.8469 (tt0) cc_final: 0.7879 (tt0) REVERT: N 90 GLN cc_start: 0.8693 (pp30) cc_final: 0.8129 (pp30) REVERT: F 24 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8768 (ttmm) REVERT: F 35 ASN cc_start: 0.9580 (t0) cc_final: 0.9072 (t0) REVERT: F 61 GLU cc_start: 0.8634 (tp30) cc_final: 0.8324 (tp30) REVERT: W 548 MET cc_start: 0.9029 (mtm) cc_final: 0.8761 (mtp) REVERT: M 3 GLN cc_start: 0.7888 (mm110) cc_final: 0.7633 (mm110) REVERT: M 13 GLN cc_start: 0.8883 (mm110) cc_final: 0.8416 (mm-40) REVERT: M 19 ARG cc_start: 0.8444 (ttm170) cc_final: 0.7965 (ttt90) REVERT: M 91 THR cc_start: 0.8711 (t) cc_final: 0.8336 (m) REVERT: G 65 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8491 (mmmm) REVERT: G 68 PHE cc_start: 0.8208 (m-10) cc_final: 0.6592 (m-10) REVERT: G 76 LYS cc_start: 0.9540 (mtpp) cc_final: 0.9280 (mttt) REVERT: G 83 MET cc_start: 0.8753 (mmm) cc_final: 0.8132 (mmt) REVERT: H 4 MET cc_start: 0.8290 (tpp) cc_final: 0.7926 (mmm) REVERT: H 17 ASP cc_start: 0.7140 (t0) cc_final: 0.6860 (t0) REVERT: H 23 CYS cc_start: 0.4745 (t) cc_final: 0.2709 (t) REVERT: H 27 GLN cc_start: 0.8429 (mt0) cc_final: 0.8017 (mp10) REVERT: P 3 GLN cc_start: 0.7732 (mp10) cc_final: 0.7358 (mp10) REVERT: P 38 GLN cc_start: 0.8479 (tt0) cc_final: 0.8268 (tt0) REVERT: P 61 ARG cc_start: 0.8792 (ptp90) cc_final: 0.8313 (ptp90) REVERT: P 62 PHE cc_start: 0.9012 (m-80) cc_final: 0.8668 (m-80) REVERT: P 90 GLN cc_start: 0.8389 (pp30) cc_final: 0.7951 (pp30) REVERT: O 34 MET cc_start: 0.8567 (mmt) cc_final: 0.7897 (mmp) REVERT: O 39 GLN cc_start: 0.7726 (tt0) cc_final: 0.7462 (tt0) REVERT: O 50 THR cc_start: 0.8682 (m) cc_final: 0.8459 (m) REVERT: O 74 ASN cc_start: 0.8017 (p0) cc_final: 0.7351 (m-40) REVERT: V 527 ILE cc_start: 0.8232 (mm) cc_final: 0.7919 (mm) REVERT: V 540 GLU cc_start: 0.8986 (mp0) cc_final: 0.8628 (pm20) REVERT: X 560 GLN cc_start: 0.9086 (tp40) cc_final: 0.8857 (tp40) REVERT: X 567 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8284 (tp40) REVERT: I 19 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8176 (ttp80) REVERT: I 25 SER cc_start: 0.7736 (t) cc_final: 0.7409 (p) REVERT: I 32 TYR cc_start: 0.7215 (m-80) cc_final: 0.6660 (m-80) REVERT: I 53 HIS cc_start: 0.8568 (p90) cc_final: 0.8305 (p90) REVERT: I 57 ASP cc_start: 0.8474 (t0) cc_final: 0.8089 (t0) REVERT: I 99 ASN cc_start: 0.8092 (t0) cc_final: 0.7326 (t0) REVERT: J 45 LYS cc_start: 0.8392 (mptt) cc_final: 0.8183 (mmtt) REVERT: J 48 ILE cc_start: 0.7727 (mp) cc_final: 0.7476 (tt) REVERT: J 87 TYR cc_start: 0.7246 (m-80) cc_final: 0.6827 (m-80) REVERT: E 58 TYR cc_start: 0.8764 (m-80) cc_final: 0.8429 (m-80) REVERT: B 35 ASN cc_start: 0.9651 (t0) cc_final: 0.9286 (t0) REVERT: D 4 MET cc_start: 0.9199 (mmm) cc_final: 0.7939 (mmm) outliers start: 58 outliers final: 48 residues processed: 425 average time/residue: 0.1606 time to fit residues: 107.0897 Evaluate side-chains 429 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 379 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 197 HIS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain V residue 610 ILE Chi-restraints excluded: chain X residue 567 GLN Chi-restraints excluded: chain X residue 581 THR Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 229 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN W 508 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.097125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.071296 restraints weight = 65309.645| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.53 r_work: 0.2835 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23214 Z= 0.204 Angle : 0.661 15.604 31575 Z= 0.335 Chirality : 0.044 0.300 3500 Planarity : 0.004 0.049 3986 Dihedral : 4.932 22.897 3124 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.33 % Allowed : 15.50 % Favored : 82.17 % 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: -0.42 (0.16), residues: 2817 helix: 0.94 (0.39), residues: 200 sheet: -0.10 (0.16), residues: 987 loop : -0.49 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 18 TYR 0.025 0.001 TYR T 162 PHE 0.021 0.001 PHE S 234 TRP 0.020 0.001 TRP U 288 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (23158) covalent geometry : angle 0.64826 / 0.33 (31437) SS BOND : bond 0.00332 / 0.23 ( 30) SS BOND : angle 1.92267 / 1.11 ( 60) hydrogen bonds : bond 0.03397 / 2.30 ( 753) hydrogen bonds : angle 5.51928 / 3.86 ( 2007) link_ALPHA1-3 : bond 0.00241 / 0.12 ( 3) link_ALPHA1-3 : angle 2.76144 / 1.43 ( 9) link_ALPHA1-6 : bond 0.00570 / 0.40 ( 6) link_ALPHA1-6 : angle 1.93017 / 1.11 ( 18) link_BETA1-4 : bond 0.00101 / 0.08 ( 6) link_BETA1-4 : angle 1.72935 / 0.96 ( 18) link_NAG-ASN : bond 0.00420 / 0.29 ( 11) link_NAG-ASN : angle 2.24191 / 1.57 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 391 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8558 (tm-30) cc_final: 0.7852 (tm-30) REVERT: T 127 ASP cc_start: 0.8981 (p0) cc_final: 0.8709 (p0) REVERT: S 51 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8195 (tt) REVERT: S 251 GLN cc_start: 0.8287 (mp10) cc_final: 0.7918 (mp10) REVERT: U 221 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8145 (mm-40) REVERT: R 4 MET cc_start: 0.8566 (mmp) cc_final: 0.8214 (mmp) REVERT: R 24 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8606 (mtp-110) REVERT: R 79 GLN cc_start: 0.7570 (mp10) cc_final: 0.7083 (mp10) REVERT: R 105 ILE cc_start: 0.7679 (tp) cc_final: 0.7399 (tp) REVERT: N 3 GLN cc_start: 0.8435 (mp10) cc_final: 0.8034 (mp10) REVERT: N 27 GLN cc_start: 0.8007 (mp10) cc_final: 0.7428 (mp10) REVERT: N 45 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8255 (ptmm) REVERT: N 61 ARG cc_start: 0.8498 (mtm110) cc_final: 0.7574 (ptp90) REVERT: N 75 ILE cc_start: 0.8823 (mp) cc_final: 0.8500 (mm) REVERT: N 82 ASP cc_start: 0.7963 (m-30) cc_final: 0.7393 (m-30) REVERT: N 89 GLN cc_start: 0.8447 (tt0) cc_final: 0.7894 (tt0) REVERT: N 90 GLN cc_start: 0.8718 (pp30) cc_final: 0.8016 (pp30) REVERT: F 24 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8756 (ttmm) REVERT: F 35 ASN cc_start: 0.9585 (t0) cc_final: 0.8911 (t0) REVERT: F 61 GLU cc_start: 0.8677 (tp30) cc_final: 0.8360 (tp30) REVERT: W 508 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: W 548 MET cc_start: 0.9018 (mtm) cc_final: 0.8736 (mtp) REVERT: W 552 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8003 (t0) REVERT: M 13 GLN cc_start: 0.8873 (mm110) cc_final: 0.8435 (mm-40) REVERT: M 19 ARG cc_start: 0.8436 (ttm170) cc_final: 0.7967 (ttt90) REVERT: M 91 THR cc_start: 0.8720 (t) cc_final: 0.8399 (m) REVERT: G 65 LYS cc_start: 0.8797 (mmmm) cc_final: 0.8475 (mmmm) REVERT: G 68 PHE cc_start: 0.8185 (m-10) cc_final: 0.6637 (m-10) REVERT: G 76 LYS cc_start: 0.9543 (mtpp) cc_final: 0.9283 (mttt) REVERT: G 83 MET cc_start: 0.8776 (mmm) cc_final: 0.8177 (mmt) REVERT: H 4 MET cc_start: 0.8293 (tpp) cc_final: 0.7919 (mmm) REVERT: H 17 ASP cc_start: 0.7295 (t0) cc_final: 0.7019 (t0) REVERT: H 23 CYS cc_start: 0.4797 (t) cc_final: 0.3111 (t) REVERT: H 27 GLN cc_start: 0.8393 (mt0) cc_final: 0.7945 (mp10) REVERT: H 32 TYR cc_start: 0.8434 (m-10) cc_final: 0.8107 (m-10) REVERT: P 3 GLN cc_start: 0.7755 (mp10) cc_final: 0.7360 (mp10) REVERT: P 27 GLN cc_start: 0.7176 (mp10) cc_final: 0.6747 (mp10) REVERT: P 61 ARG cc_start: 0.8797 (ptp90) cc_final: 0.8278 (ptp90) REVERT: P 62 PHE cc_start: 0.9024 (m-80) cc_final: 0.8688 (m-80) REVERT: P 90 GLN cc_start: 0.8398 (pp30) cc_final: 0.8014 (pp30) REVERT: O 34 MET cc_start: 0.8599 (mmt) cc_final: 0.7926 (mmp) REVERT: O 50 THR cc_start: 0.8654 (m) cc_final: 0.8443 (m) REVERT: O 74 ASN cc_start: 0.7971 (p0) cc_final: 0.7330 (m-40) REVERT: V 527 ILE cc_start: 0.8272 (mm) cc_final: 0.7959 (mm) REVERT: V 540 GLU cc_start: 0.8998 (mp0) cc_final: 0.8619 (pm20) REVERT: X 560 GLN cc_start: 0.9065 (tp40) cc_final: 0.8828 (tp40) REVERT: X 567 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8284 (tp40) REVERT: X 596 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7614 (ttm110) REVERT: I 25 SER cc_start: 0.7686 (t) cc_final: 0.7369 (p) REVERT: I 32 TYR cc_start: 0.7200 (m-80) cc_final: 0.6622 (m-80) REVERT: I 57 ASP cc_start: 0.8524 (t0) cc_final: 0.8135 (t0) REVERT: I 99 ASN cc_start: 0.8026 (t0) cc_final: 0.7279 (t0) REVERT: J 45 LYS cc_start: 0.8330 (mptt) cc_final: 0.8122 (mmtt) REVERT: J 48 ILE cc_start: 0.7719 (mp) cc_final: 0.7447 (tt) REVERT: J 87 TYR cc_start: 0.7091 (m-80) cc_final: 0.6694 (m-80) REVERT: E 58 TYR cc_start: 0.8771 (m-80) cc_final: 0.8476 (m-80) REVERT: B 35 ASN cc_start: 0.9641 (t0) cc_final: 0.9317 (t0) REVERT: D 4 MET cc_start: 0.9182 (mmm) cc_final: 0.7870 (mmm) outliers start: 56 outliers final: 46 residues processed: 426 average time/residue: 0.1558 time to fit residues: 104.3371 Evaluate side-chains 426 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 375 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 197 HIS Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain W residue 508 GLN Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 552 ASP Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain X residue 567 GLN Chi-restraints excluded: chain X residue 581 THR Chi-restraints excluded: chain X residue 596 ARG Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 27 optimal weight: 0.0980 chunk 162 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN W 508 GLN M 3 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.097468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071485 restraints weight = 65436.778| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.57 r_work: 0.2841 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23214 Z= 0.186 Angle : 0.669 15.595 31575 Z= 0.338 Chirality : 0.044 0.301 3500 Planarity : 0.004 0.050 3986 Dihedral : 4.900 23.313 3124 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.41 % Allowed : 15.96 % Favored : 81.63 % 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: -0.44 (0.16), residues: 2817 helix: 0.94 (0.39), residues: 200 sheet: -0.09 (0.16), residues: 991 loop : -0.53 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 24 TYR 0.032 0.001 TYR M 32 PHE 0.022 0.001 PHE S 234 TRP 0.018 0.001 TRP U 288 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (23158) covalent geometry : angle 0.65648 / 0.33 (31437) SS BOND : bond 0.00390 / 0.32 ( 30) SS BOND : angle 1.99760 / 1.14 ( 60) hydrogen bonds : bond 0.03330 / 2.26 ( 753) hydrogen bonds : angle 5.46784 / 3.82 ( 2007) link_ALPHA1-3 : bond 0.00242 / 0.12 ( 3) link_ALPHA1-3 : angle 2.72747 / 1.41 ( 9) link_ALPHA1-6 : bond 0.00611 / 0.46 ( 6) link_ALPHA1-6 : angle 1.90282 / 1.09 ( 18) link_BETA1-4 : bond 0.00103 / 0.06 ( 6) link_BETA1-4 : angle 1.69600 / 0.94 ( 18) link_NAG-ASN : bond 0.00395 / 0.27 ( 11) link_NAG-ASN : angle 2.19134 / 1.53 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 388 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7854 (tm-30) REVERT: T 127 ASP cc_start: 0.8951 (p0) cc_final: 0.8660 (p0) REVERT: S 251 GLN cc_start: 0.8222 (mp10) cc_final: 0.7956 (mp10) REVERT: U 221 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8101 (mm-40) REVERT: R 4 MET cc_start: 0.8568 (mmp) cc_final: 0.8238 (mmp) REVERT: R 24 ARG cc_start: 0.8879 (mtp-110) cc_final: 0.8616 (mtp-110) REVERT: R 42 LYS cc_start: 0.8371 (mppt) cc_final: 0.7631 (mppt) REVERT: R 79 GLN cc_start: 0.7570 (mp10) cc_final: 0.7060 (mp10) REVERT: R 105 ILE cc_start: 0.7565 (tp) cc_final: 0.7287 (tp) REVERT: N 3 GLN cc_start: 0.8413 (mp10) cc_final: 0.8031 (mp10) REVERT: N 27 GLN cc_start: 0.8023 (mp10) cc_final: 0.7427 (mp10) REVERT: N 45 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8260 (ptmm) REVERT: N 61 ARG cc_start: 0.8504 (mtm110) cc_final: 0.7582 (ptp90) REVERT: N 75 ILE cc_start: 0.8790 (mp) cc_final: 0.8469 (mm) REVERT: N 82 ASP cc_start: 0.7956 (m-30) cc_final: 0.7415 (m-30) REVERT: N 89 GLN cc_start: 0.8451 (tt0) cc_final: 0.7890 (tt0) REVERT: N 90 GLN cc_start: 0.8655 (pp30) cc_final: 0.8091 (pp30) REVERT: F 24 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8751 (ttmm) REVERT: F 35 ASN cc_start: 0.9565 (t0) cc_final: 0.8884 (t0) REVERT: F 61 GLU cc_start: 0.8667 (tp30) cc_final: 0.8349 (tp30) REVERT: W 548 MET cc_start: 0.9016 (mtm) cc_final: 0.8750 (mtp) REVERT: W 552 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7989 (t0) REVERT: M 3 GLN cc_start: 0.7861 (mm110) cc_final: 0.7635 (mm110) REVERT: M 13 GLN cc_start: 0.8892 (mm110) cc_final: 0.8407 (mm-40) REVERT: M 19 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8027 (ttt90) REVERT: M 87 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7481 (mtt90) REVERT: M 91 THR cc_start: 0.8706 (t) cc_final: 0.8312 (m) REVERT: G 65 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8466 (mmmm) REVERT: G 68 PHE cc_start: 0.8157 (m-10) cc_final: 0.6627 (m-10) REVERT: G 76 LYS cc_start: 0.9539 (mtpp) cc_final: 0.9280 (mttt) REVERT: G 83 MET cc_start: 0.8730 (mmm) cc_final: 0.8059 (mmt) REVERT: H 4 MET cc_start: 0.8276 (tpp) cc_final: 0.7941 (mmm) REVERT: H 17 ASP cc_start: 0.7206 (t0) cc_final: 0.6954 (t0) REVERT: H 18 ARG cc_start: 0.8224 (tpm170) cc_final: 0.7889 (tpt90) REVERT: H 23 CYS cc_start: 0.5295 (t) cc_final: 0.3103 (t) REVERT: H 27 GLN cc_start: 0.8402 (mt0) cc_final: 0.7928 (mp10) REVERT: H 32 TYR cc_start: 0.8432 (m-10) cc_final: 0.8107 (m-10) REVERT: P 3 GLN cc_start: 0.7722 (mp10) cc_final: 0.7332 (mp10) REVERT: P 61 ARG cc_start: 0.8802 (ptp90) cc_final: 0.8256 (ptp90) REVERT: P 62 PHE cc_start: 0.8984 (m-80) cc_final: 0.8649 (m-80) REVERT: P 90 GLN cc_start: 0.8345 (pp30) cc_final: 0.7890 (pp30) REVERT: O 34 MET cc_start: 0.8672 (mmt) cc_final: 0.7989 (mmp) REVERT: O 74 ASN cc_start: 0.7984 (p0) cc_final: 0.7409 (m-40) REVERT: V 527 ILE cc_start: 0.8315 (mm) cc_final: 0.8027 (mm) REVERT: V 540 GLU cc_start: 0.8996 (mp0) cc_final: 0.8617 (pm20) REVERT: X 560 GLN cc_start: 0.9035 (tp40) cc_final: 0.8808 (tp40) REVERT: X 567 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8280 (tp40) REVERT: X 596 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7630 (ttm110) REVERT: I 19 ARG cc_start: 0.8608 (ttp80) cc_final: 0.7994 (ttp80) REVERT: I 25 SER cc_start: 0.7687 (t) cc_final: 0.7333 (p) REVERT: I 32 TYR cc_start: 0.7206 (m-80) cc_final: 0.6616 (m-80) REVERT: I 57 ASP cc_start: 0.8550 (t0) cc_final: 0.8153 (t0) REVERT: I 99 ASN cc_start: 0.7934 (t0) cc_final: 0.7148 (t0) REVERT: J 45 LYS cc_start: 0.8321 (mptt) cc_final: 0.8112 (mmtt) REVERT: J 48 ILE cc_start: 0.7714 (mp) cc_final: 0.7452 (tt) REVERT: J 87 TYR cc_start: 0.7074 (m-80) cc_final: 0.6696 (m-80) REVERT: E 58 TYR cc_start: 0.8745 (m-80) cc_final: 0.8420 (m-80) REVERT: B 35 ASN cc_start: 0.9622 (t0) cc_final: 0.9336 (t0) REVERT: B 48 GLN cc_start: 0.8850 (mp10) cc_final: 0.8642 (mp10) REVERT: D 4 MET cc_start: 0.9177 (mmm) cc_final: 0.7899 (mmm) outliers start: 58 outliers final: 50 residues processed: 423 average time/residue: 0.1637 time to fit residues: 108.1516 Evaluate side-chains 430 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 377 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 197 HIS Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 552 ASP Chi-restraints excluded: chain W residue 556 CYS Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain X residue 567 GLN Chi-restraints excluded: chain X residue 581 THR Chi-restraints excluded: chain X residue 596 ARG Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 237 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 chunk 113 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 247 optimal weight: 0.0970 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Q 39 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 508 GLN I 74 ASN I 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.085094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059862 restraints weight = 67019.267| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.50 r_work: 0.2882 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23214 Z= 0.129 Angle : 0.668 15.806 31575 Z= 0.337 Chirality : 0.044 0.289 3500 Planarity : 0.004 0.049 3986 Dihedral : 4.767 22.027 3124 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.00 % Allowed : 16.83 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2817 helix: 0.93 (0.39), residues: 200 sheet: -0.00 (0.16), residues: 985 loop : -0.52 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 24 TYR 0.023 0.001 TYR U 162 PHE 0.021 0.001 PHE S 234 TRP 0.027 0.001 TRP I 36 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (23158) covalent geometry : angle 0.65811 / 0.33 (31437) SS BOND : bond 0.00312 / 0.26 ( 30) SS BOND : angle 1.65733 / 0.96 ( 60) hydrogen bonds : bond 0.03157 / 2.15 ( 753) hydrogen bonds : angle 5.33008 / 3.73 ( 2007) link_ALPHA1-3 : bond 0.00314 / 0.16 ( 3) link_ALPHA1-3 : angle 2.63127 / 1.36 ( 9) link_ALPHA1-6 : bond 0.00691 / 0.50 ( 6) link_ALPHA1-6 : angle 1.81959 / 1.04 ( 18) link_BETA1-4 : bond 0.00272 / 0.13 ( 6) link_BETA1-4 : angle 1.57894 / 0.88 ( 18) link_NAG-ASN : bond 0.00360 / 0.21 ( 11) link_NAG-ASN : angle 2.00571 / 1.40 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 402 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 34 MET cc_start: 0.8856 (mmm) cc_final: 0.8477 (mmt) REVERT: T 127 ASP cc_start: 0.8797 (p0) cc_final: 0.8531 (p0) REVERT: S 251 GLN cc_start: 0.8218 (mp10) cc_final: 0.7963 (mp10) REVERT: U 221 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8088 (mm-40) REVERT: R 4 MET cc_start: 0.8595 (mmp) cc_final: 0.8258 (mmp) REVERT: R 24 ARG cc_start: 0.8877 (mtp-110) cc_final: 0.8613 (mtp-110) REVERT: R 42 LYS cc_start: 0.8328 (mppt) cc_final: 0.7596 (mppt) REVERT: R 79 GLN cc_start: 0.7565 (mp10) cc_final: 0.7040 (mp10) REVERT: R 102 ARG cc_start: 0.8373 (ptm-80) cc_final: 0.7831 (ttp80) REVERT: R 105 ILE cc_start: 0.7627 (tp) cc_final: 0.7363 (tp) REVERT: N 3 GLN cc_start: 0.8433 (mp10) cc_final: 0.8123 (mp10) REVERT: N 27 GLN cc_start: 0.8017 (mp10) cc_final: 0.7447 (mp10) REVERT: N 45 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8344 (ptmm) REVERT: N 61 ARG cc_start: 0.8521 (mtm110) cc_final: 0.7634 (ptp90) REVERT: N 75 ILE cc_start: 0.8803 (mp) cc_final: 0.8504 (mm) REVERT: N 82 ASP cc_start: 0.7998 (m-30) cc_final: 0.7482 (m-30) REVERT: N 89 GLN cc_start: 0.8323 (tt0) cc_final: 0.7964 (tt0) REVERT: N 90 GLN cc_start: 0.8700 (pp30) cc_final: 0.8192 (pp30) REVERT: F 24 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8763 (ttmm) REVERT: F 35 ASN cc_start: 0.9569 (t0) cc_final: 0.8887 (t0) REVERT: F 61 GLU cc_start: 0.8590 (tp30) cc_final: 0.8257 (tp30) REVERT: W 548 MET cc_start: 0.9002 (mtm) cc_final: 0.8731 (mtt) REVERT: W 552 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7938 (t0) REVERT: M 3 GLN cc_start: 0.7869 (mm110) cc_final: 0.7575 (mm110) REVERT: M 13 GLN cc_start: 0.8859 (mm110) cc_final: 0.8346 (mm-40) REVERT: M 50 THR cc_start: 0.8687 (t) cc_final: 0.8276 (m) REVERT: M 73 ASP cc_start: 0.7522 (t0) cc_final: 0.7136 (t0) REVERT: M 87 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7608 (mtt90) REVERT: M 91 THR cc_start: 0.8685 (t) cc_final: 0.8330 (m) REVERT: G 65 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8451 (mmmm) REVERT: G 68 PHE cc_start: 0.8056 (m-10) cc_final: 0.6530 (m-10) REVERT: G 76 LYS cc_start: 0.9522 (mtpp) cc_final: 0.9255 (mttt) REVERT: G 80 TYR cc_start: 0.8531 (m-80) cc_final: 0.8059 (m-80) REVERT: G 83 MET cc_start: 0.8757 (mmm) cc_final: 0.8078 (mmt) REVERT: H 4 MET cc_start: 0.8267 (tpp) cc_final: 0.7925 (mmm) REVERT: H 17 ASP cc_start: 0.7231 (t0) cc_final: 0.7004 (t0) REVERT: H 18 ARG cc_start: 0.8218 (tpm170) cc_final: 0.7904 (tpt90) REVERT: H 23 CYS cc_start: 0.5119 (t) cc_final: 0.3122 (t) REVERT: H 27 GLN cc_start: 0.8443 (mt0) cc_final: 0.7965 (mp10) REVERT: H 32 TYR cc_start: 0.8469 (m-10) cc_final: 0.8109 (m-10) REVERT: P 3 GLN cc_start: 0.7801 (mp10) cc_final: 0.7408 (mp10) REVERT: P 27 GLN cc_start: 0.7233 (mp10) cc_final: 0.6778 (mp10) REVERT: P 61 ARG cc_start: 0.8834 (ptp90) cc_final: 0.8399 (ptp90) REVERT: P 90 GLN cc_start: 0.8166 (pp30) cc_final: 0.7742 (pp30) REVERT: O 34 MET cc_start: 0.8662 (mmt) cc_final: 0.8057 (mmp) REVERT: O 74 ASN cc_start: 0.7898 (p0) cc_final: 0.7573 (m-40) REVERT: V 527 ILE cc_start: 0.8136 (mm) cc_final: 0.7823 (mm) REVERT: V 540 GLU cc_start: 0.8944 (mp0) cc_final: 0.8572 (pm20) REVERT: X 560 GLN cc_start: 0.9008 (tp40) cc_final: 0.8710 (tp40) REVERT: X 567 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8171 (tp40) REVERT: X 596 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7838 (ttm110) REVERT: I 19 ARG cc_start: 0.8588 (ttp80) cc_final: 0.7936 (ttp80) REVERT: I 25 SER cc_start: 0.7678 (t) cc_final: 0.7327 (p) REVERT: I 32 TYR cc_start: 0.7175 (m-80) cc_final: 0.6608 (m-80) REVERT: I 57 ASP cc_start: 0.8589 (t0) cc_final: 0.8205 (t0) REVERT: I 99 ASN cc_start: 0.8126 (t0) cc_final: 0.7320 (t0) REVERT: J 48 ILE cc_start: 0.7705 (mp) cc_final: 0.7489 (tt) REVERT: J 87 TYR cc_start: 0.7110 (m-80) cc_final: 0.6723 (m-80) REVERT: E 46 GLU cc_start: 0.8826 (tt0) cc_final: 0.8556 (pt0) REVERT: E 58 TYR cc_start: 0.8655 (m-80) cc_final: 0.8406 (m-80) REVERT: B 24 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8540 (ttmm) REVERT: B 35 ASN cc_start: 0.9619 (t0) cc_final: 0.9349 (t0) REVERT: B 48 GLN cc_start: 0.8792 (mp10) cc_final: 0.8517 (mp10) REVERT: D 4 MET cc_start: 0.9199 (mmm) cc_final: 0.7886 (mmm) outliers start: 48 outliers final: 39 residues processed: 431 average time/residue: 0.1474 time to fit residues: 100.2191 Evaluate side-chains 425 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 383 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain T residue 162 TYR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 244 LEU Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain W residue 544 THR Chi-restraints excluded: chain W residue 552 ASP Chi-restraints excluded: chain W residue 579 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain X residue 567 GLN Chi-restraints excluded: chain X residue 581 THR Chi-restraints excluded: chain X residue 596 ARG Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.097737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.071801 restraints weight = 65371.247| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.52 r_work: 0.2851 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23214 Z= 0.203 Angle : 0.681 15.537 31575 Z= 0.345 Chirality : 0.044 0.287 3500 Planarity : 0.004 0.049 3986 Dihedral : 4.821 21.654 3124 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.95 % Allowed : 17.37 % Favored : 80.67 % 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: -0.43 (0.16), residues: 2817 helix: 1.30 (0.40), residues: 188 sheet: -0.07 (0.16), residues: 995 loop : -0.56 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 18 TYR 0.027 0.002 TYR M 32 PHE 0.021 0.001 PHE S 234 TRP 0.022 0.001 TRP U 288 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (23158) covalent geometry : angle 0.67038 / 0.34 (31437) SS BOND : bond 0.00350 / 0.27 ( 30) SS BOND : angle 1.73597 / 1.02 ( 60) hydrogen bonds : bond 0.03337 / 2.28 ( 753) hydrogen bonds : angle 5.32282 / 3.72 ( 2007) link_ALPHA1-3 : bond 0.00187 / 0.09 ( 3) link_ALPHA1-3 : angle 2.68055 / 1.38 ( 9) link_ALPHA1-6 : bond 0.00513 / 0.32 ( 6) link_ALPHA1-6 : angle 1.87642 / 1.08 ( 18) link_BETA1-4 : bond 0.00097 / 0.06 ( 6) link_BETA1-4 : angle 1.67473 / 0.93 ( 18) link_NAG-ASN : bond 0.00374 / 0.26 ( 11) link_NAG-ASN : angle 2.10452 / 1.47 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6461.34 seconds wall clock time: 111 minutes 40.10 seconds (6700.10 seconds total)