Starting phenix.real_space_refine on Sun Dec 29 05:35:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsv_44873/12_2024/9bsv_44873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsv_44873/12_2024/9bsv_44873.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bsv_44873/12_2024/9bsv_44873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsv_44873/12_2024/9bsv_44873.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsv_44873/12_2024/9bsv_44873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsv_44873/12_2024/9bsv_44873.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.016 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 45 5.16 5 C 6228 2.51 5 N 1695 2.21 5 O 1911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9879 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 938 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "A" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain breaks: 2 Chain: "B" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain breaks: 2 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain breaks: 2 Chain: "E" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 938 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 938 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.49, per 1000 atoms: 0.66 Number of scatterers: 9879 At special positions: 0 Unit cell: (113.323, 109.781, 91.1893, 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 45 16.00 O 1911 8.00 N 1695 7.00 C 6228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 556 " distance=2.04 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 609 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 511 " - pdb=" SG CYS C 556 " distance=2.04 Simple disulfide: pdb=" SG CYS C 601 " - pdb=" SG CYS C 608 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " 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=1, symmetry=0 Links applied ALPHA1-2 " MAN H 4 " - " MAN H 5 " ALPHA1-3 " MAN G 3 " - " MAN G 7 " " BMA H 3 " - " MAN H 7 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " ALPHA1-4 " NAG G 2 " - " MAN G 3 " " MAN G 4 " - " MAN G 5 " ALPHA1-6 " MAN G 3 " - " MAN G 4 " " MAN G 4 " - " MAN G 6 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " MAN H 4 " - " BMA H 6 " NAG-ASN " NAG G 1 " - " ASN A 563 " " NAG H 1 " - " ASN B 563 " " NAG I 1 " - " ASN C 563 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 25 sheets defined 16.2% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.785A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.652A pdb=" N THR D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 110' Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.968A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 576 removed outlier: 5.179A pdb=" N GLN A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ALA A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 597 removed outlier: 3.645A pdb=" N ARG A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.896A pdb=" N LYS B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 565 through 576 Processing helix chain 'B' and resid 583 through 597 removed outlier: 3.723A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.650A pdb=" N GLY C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 78 through 84 removed outlier: 4.100A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 565 through 576 Processing helix chain 'C' and resid 584 through 597 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.720A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 removed outlier: 3.679A pdb=" N THR E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR E 110 " --> pdb=" O ALA E 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 106 through 110' Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.652A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.762A pdb=" N THR F 109 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR F 110 " --> pdb=" O ALA F 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 110' Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.530A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.221A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER D 122 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 12 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 59 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.221A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER D 122 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 12 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.459A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.459A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A 96 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.643A pdb=" N TRP A 518 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.448A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.448A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 46 removed outlier: 3.536A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 46 removed outlier: 3.536A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 177 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB4, first strand: chain 'B' and resid 105 through 111 removed outlier: 6.307A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 518 through 519 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 45 removed outlier: 6.654A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 45 removed outlier: 6.654A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 177 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 96 " --> pdb=" O THR C 581 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB9, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AC1, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.312A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.237A pdb=" N GLY E 10 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER E 122 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 12 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP E 36 " --> pdb=" O ALA E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.237A pdb=" N GLY E 10 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER E 122 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 12 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.960A pdb=" N VAL F 12 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP F 36 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 59 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.960A pdb=" N VAL F 12 " --> pdb=" O SER F 122 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 741 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: 3.19 Time building geometry restraints manager: 3.22 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: 3196 1.34 - 1.46: 2509 1.46 - 1.58: 4351 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 10110 Sorted by residual: bond pdb=" N ARG F 99 " pdb=" CA ARG F 99 " ideal model delta sigma weight residual 1.455 1.486 -0.032 9.60e-03 1.09e+04 1.08e+01 bond pdb=" N ARG E 99 " pdb=" CA ARG E 99 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.53e+00 bond pdb=" N ARG D 99 " pdb=" CA ARG D 99 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.04e-02 9.25e+03 8.07e+00 bond pdb=" N ILE E 103 " pdb=" CA ILE E 103 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.36e+00 bond pdb=" N TRP D 101 " pdb=" CA TRP D 101 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.24e-02 6.50e+03 7.33e+00 ... (remaining 10105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 13034 1.41 - 2.82: 507 2.82 - 4.23: 138 4.23 - 5.64: 35 5.64 - 7.05: 11 Bond angle restraints: 13725 Sorted by residual: angle pdb=" CA TRP D 101 " pdb=" C TRP D 101 " pdb=" O TRP D 101 " ideal model delta sigma weight residual 120.88 115.27 5.61 9.40e-01 1.13e+00 3.56e+01 angle pdb=" CA PRO F 100 " pdb=" C PRO F 100 " pdb=" O PRO F 100 " ideal model delta sigma weight residual 121.11 115.48 5.63 1.08e+00 8.57e-01 2.72e+01 angle pdb=" C ARG D 99 " pdb=" CA ARG D 99 " pdb=" CB ARG D 99 " ideal model delta sigma weight residual 110.22 104.03 6.19 1.32e+00 5.74e-01 2.20e+01 angle pdb=" N ARG D 99 " pdb=" CA ARG D 99 " pdb=" CB ARG D 99 " ideal model delta sigma weight residual 111.10 106.92 4.18 1.05e+00 9.07e-01 1.58e+01 angle pdb=" O PRO F 100 " pdb=" C PRO F 100 " pdb=" N TRP F 101 " ideal model delta sigma weight residual 122.73 125.54 -2.81 7.10e-01 1.98e+00 1.56e+01 ... (remaining 13720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.76: 5876 26.76 - 53.51: 232 53.51 - 80.27: 48 80.27 - 107.03: 54 107.03 - 133.78: 20 Dihedral angle restraints: 6230 sinusoidal: 2684 harmonic: 3546 Sorted by residual: dihedral pdb=" CB CYS A 601 " pdb=" SG CYS A 601 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual -86.00 -2.71 -83.29 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS C 601 " pdb=" SG CYS C 601 " pdb=" SG CYS C 608 " pdb=" CB CYS C 608 " ideal model delta sinusoidal sigma weight residual -86.00 -17.76 -68.24 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" CD ARG D 99 " pdb=" NE ARG D 99 " pdb=" CZ ARG D 99 " pdb=" NH1 ARG D 99 " ideal model delta sinusoidal sigma weight residual 0.00 -63.10 63.10 1 1.00e+01 1.00e-02 5.26e+01 ... (remaining 6227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1507 0.123 - 0.246: 30 0.246 - 0.369: 4 0.369 - 0.492: 4 0.492 - 0.615: 2 Chirality restraints: 1547 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.46e+02 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.66e+02 chirality pdb=" C1 MAN G 4 " pdb=" O6 MAN G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 2.11 0.29 2.00e-02 2.50e+03 2.11e+02 ... (remaining 1544 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.148 2.00e-02 2.50e+03 1.23e-01 1.89e+02 pdb=" C7 NAG H 2 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.110 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.198 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 99 " 0.986 9.50e-02 1.11e+02 4.42e-01 1.18e+02 pdb=" NE ARG D 99 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG D 99 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 99 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 99 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.056 2.00e-02 2.50e+03 4.58e-02 2.62e+01 pdb=" C7 NAG I 2 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.073 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.010 2.00e-02 2.50e+03 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 40 2.44 - 3.05: 6057 3.05 - 3.67: 13664 3.67 - 4.28: 20635 4.28 - 4.90: 35753 Nonbonded interactions: 76149 Sorted by model distance: nonbonded pdb=" OE1 GLN A 521 " pdb=" CD1 ILE A 544 " model vdw 1.819 3.460 nonbonded pdb=" O6 MAN I 4 " pdb=" O6 MAN E 201 " model vdw 1.828 3.040 nonbonded pdb=" O6 MAN I 4 " pdb=" C6 MAN E 201 " model vdw 2.134 2.752 nonbonded pdb=" OD1 ASP C 163 " pdb=" OH TYR C 543 " model vdw 2.150 3.040 nonbonded pdb=" NE2 GLN A 521 " pdb=" OD1 ASP A 522 " model vdw 2.200 3.120 ... (remaining 76144 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 123) selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 or resid 5 or resid 7)) selection = (chain 'H' and (resid 2 or resid 5 or resid 7)) selection = (chain 'I' and (resid 1 or resid 4 or resid 6)) } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.870 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 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 : 0.005 0.036 10110 Z= 0.302 Angle : 0.705 7.055 13725 Z= 0.386 Chirality : 0.058 0.615 1547 Planarity : 0.012 0.442 1755 Dihedral : 19.517 133.783 3923 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.74 % Allowed : 4.17 % Favored : 95.10 % Rotamer: Outliers : 0.69 % Allowed : 0.69 % Favored : 98.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1224 helix: 2.14 (0.49), residues: 117 sheet: -0.15 (0.28), residues: 339 loop : -1.09 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 597 HIS 0.005 0.001 HIS C 549 PHE 0.022 0.001 PHE A 193 TYR 0.017 0.001 TYR A 162 ARG 0.004 0.000 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9051 (tttp) cc_final: 0.8754 (ttpt) REVERT: A 140 LYS cc_start: 0.8739 (mttm) cc_final: 0.8356 (mttp) REVERT: B 44 GLN cc_start: 0.8672 (mt0) cc_final: 0.8471 (mt0) REVERT: B 56 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8215 (mmtt) REVERT: E 65 LYS cc_start: 0.9106 (tttp) cc_final: 0.8875 (ttpt) REVERT: E 73 ASP cc_start: 0.8850 (t0) cc_final: 0.8322 (t0) outliers start: 7 outliers final: 2 residues processed: 178 average time/residue: 0.3399 time to fit residues: 76.8592 Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain E residue 101 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0010 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 ASN A 567 GLN B 549 HIS B 567 GLN C 62 GLN E 105 ASN F 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10110 Z= 0.308 Angle : 0.650 8.121 13725 Z= 0.324 Chirality : 0.047 0.228 1547 Planarity : 0.005 0.051 1755 Dihedral : 18.180 129.952 1773 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.25 % Favored : 95.18 % Rotamer: Outliers : 1.19 % Allowed : 7.34 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1224 helix: 2.43 (0.50), residues: 120 sheet: -0.31 (0.25), residues: 387 loop : -1.02 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 101 HIS 0.003 0.001 HIS A 516 PHE 0.020 0.002 PHE A 193 TYR 0.028 0.001 TYR A 162 ARG 0.006 0.001 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9059 (tttp) cc_final: 0.8744 (ttmt) REVERT: D 73 ASP cc_start: 0.8595 (t0) cc_final: 0.7919 (t0) REVERT: D 105 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8414 (m-40) REVERT: A 140 LYS cc_start: 0.8800 (mttm) cc_final: 0.8397 (mttp) REVERT: E 3 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8631 (mp10) REVERT: E 65 LYS cc_start: 0.9123 (tttp) cc_final: 0.8870 (ttpt) REVERT: F 6 GLU cc_start: 0.8856 (mp0) cc_final: 0.8636 (mp0) outliers start: 12 outliers final: 10 residues processed: 136 average time/residue: 0.3122 time to fit residues: 55.1552 Evaluate side-chains 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 111 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 ASN B 549 HIS C 506 ASN C 549 HIS E 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10110 Z= 0.196 Angle : 0.581 7.708 13725 Z= 0.289 Chirality : 0.044 0.223 1547 Planarity : 0.004 0.042 1755 Dihedral : 15.965 130.539 1773 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.08 % Favored : 95.51 % Rotamer: Outliers : 1.59 % Allowed : 7.94 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1224 helix: 2.17 (0.49), residues: 138 sheet: -0.31 (0.24), residues: 387 loop : -0.96 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 597 HIS 0.004 0.001 HIS B 549 PHE 0.018 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.005 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9045 (tttp) cc_final: 0.8732 (ttpt) REVERT: D 73 ASP cc_start: 0.8609 (t0) cc_final: 0.7889 (t0) REVERT: A 140 LYS cc_start: 0.8799 (mttm) cc_final: 0.8404 (mttp) REVERT: A 597 TRP cc_start: 0.6609 (m-90) cc_final: 0.6407 (m-90) REVERT: E 65 LYS cc_start: 0.9103 (tttp) cc_final: 0.8856 (ttpt) REVERT: E 120 THR cc_start: 0.9191 (m) cc_final: 0.8861 (p) REVERT: F 6 GLU cc_start: 0.8803 (mp0) cc_final: 0.8544 (mp0) REVERT: F 57 ARG cc_start: 0.8740 (tpt90) cc_final: 0.8526 (tpt-90) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 0.3018 time to fit residues: 53.9881 Evaluate side-chains 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 ASN D 118 GLN ** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10110 Z= 0.304 Angle : 0.594 8.499 13725 Z= 0.298 Chirality : 0.045 0.216 1547 Planarity : 0.004 0.040 1755 Dihedral : 15.282 130.123 1773 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.41 % Favored : 95.18 % Rotamer: Outliers : 1.59 % Allowed : 9.03 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1224 helix: 2.20 (0.50), residues: 138 sheet: -0.29 (0.24), residues: 387 loop : -0.99 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 597 HIS 0.006 0.001 HIS B 549 PHE 0.021 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.004 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9046 (tttp) cc_final: 0.8730 (ttmt) REVERT: D 73 ASP cc_start: 0.8663 (t0) cc_final: 0.7926 (t0) REVERT: D 105 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8518 (m-40) REVERT: A 140 LYS cc_start: 0.8822 (mttm) cc_final: 0.8428 (mttp) REVERT: E 65 LYS cc_start: 0.9100 (tttp) cc_final: 0.8837 (ttpt) REVERT: E 120 THR cc_start: 0.9195 (m) cc_final: 0.8884 (p) REVERT: F 6 GLU cc_start: 0.8762 (mp0) cc_final: 0.8429 (mp0) outliers start: 16 outliers final: 13 residues processed: 128 average time/residue: 0.3193 time to fit residues: 53.4672 Evaluate side-chains 130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 0.0010 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 ASN B 549 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10110 Z= 0.200 Angle : 0.563 8.887 13725 Z= 0.281 Chirality : 0.044 0.233 1547 Planarity : 0.004 0.039 1755 Dihedral : 14.715 127.894 1773 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.92 % Favored : 95.67 % Rotamer: Outliers : 1.59 % Allowed : 9.72 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1224 helix: 2.18 (0.50), residues: 138 sheet: -0.24 (0.24), residues: 387 loop : -0.95 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 597 HIS 0.005 0.001 HIS B 549 PHE 0.018 0.001 PHE A 193 TYR 0.022 0.001 TYR A 162 ARG 0.005 0.000 ARG F 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9034 (tttp) cc_final: 0.8722 (ttpt) REVERT: D 73 ASP cc_start: 0.8669 (t0) cc_final: 0.7923 (t0) REVERT: D 105 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8485 (m-40) REVERT: A 140 LYS cc_start: 0.8823 (mttm) cc_final: 0.8433 (mttp) REVERT: E 65 LYS cc_start: 0.9079 (tttp) cc_final: 0.8824 (ttpt) REVERT: E 120 THR cc_start: 0.9180 (m) cc_final: 0.8902 (p) REVERT: F 6 GLU cc_start: 0.8740 (mp0) cc_final: 0.8410 (mp0) outliers start: 16 outliers final: 14 residues processed: 138 average time/residue: 0.3011 time to fit residues: 54.7547 Evaluate side-chains 134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 114 optimal weight: 3.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 ASN B 549 HIS C 549 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10110 Z= 0.349 Angle : 0.610 8.639 13725 Z= 0.304 Chirality : 0.045 0.217 1547 Planarity : 0.004 0.039 1755 Dihedral : 14.531 127.068 1773 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.49 % Favored : 95.02 % Rotamer: Outliers : 2.08 % Allowed : 10.71 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1224 helix: 2.19 (0.50), residues: 138 sheet: -0.30 (0.25), residues: 363 loop : -0.97 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 597 HIS 0.019 0.001 HIS B 549 PHE 0.022 0.002 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.005 0.000 ARG F 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9058 (tttp) cc_final: 0.8725 (ttpt) REVERT: D 73 ASP cc_start: 0.8717 (t0) cc_final: 0.7938 (t0) REVERT: A 140 LYS cc_start: 0.8822 (mttm) cc_final: 0.8430 (mttp) REVERT: A 597 TRP cc_start: 0.6682 (m-90) cc_final: 0.6465 (m-90) REVERT: C 184 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8951 (pp) REVERT: E 65 LYS cc_start: 0.9100 (tttp) cc_final: 0.8832 (ttpt) REVERT: E 120 THR cc_start: 0.9194 (m) cc_final: 0.8908 (p) REVERT: F 6 GLU cc_start: 0.8727 (mp0) cc_final: 0.8312 (mp0) outliers start: 21 outliers final: 15 residues processed: 137 average time/residue: 0.2805 time to fit residues: 51.2287 Evaluate side-chains 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.0470 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 HIS C 549 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10110 Z= 0.190 Angle : 0.575 8.580 13725 Z= 0.285 Chirality : 0.044 0.225 1547 Planarity : 0.004 0.038 1755 Dihedral : 14.019 126.733 1773 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.08 % Favored : 95.51 % Rotamer: Outliers : 1.49 % Allowed : 11.21 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1224 helix: 2.18 (0.50), residues: 138 sheet: -0.21 (0.24), residues: 387 loop : -0.96 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 597 HIS 0.018 0.001 HIS B 549 PHE 0.017 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.004 0.000 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9040 (tttp) cc_final: 0.8711 (ttpt) REVERT: D 73 ASP cc_start: 0.8707 (t0) cc_final: 0.7958 (t0) REVERT: A 140 LYS cc_start: 0.8848 (mttm) cc_final: 0.8452 (mttp) REVERT: C 184 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8970 (pp) REVERT: E 65 LYS cc_start: 0.9087 (tttp) cc_final: 0.8826 (ttpt) REVERT: E 120 THR cc_start: 0.9185 (m) cc_final: 0.8930 (p) REVERT: F 6 GLU cc_start: 0.8712 (mp0) cc_final: 0.8312 (mp0) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.2890 time to fit residues: 50.9215 Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 HIS C 549 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10110 Z= 0.296 Angle : 0.604 7.961 13725 Z= 0.299 Chirality : 0.045 0.207 1547 Planarity : 0.004 0.041 1755 Dihedral : 13.776 127.194 1773 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.41 % Favored : 95.10 % Rotamer: Outliers : 1.49 % Allowed : 11.61 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1224 helix: 2.22 (0.50), residues: 138 sheet: -0.32 (0.25), residues: 366 loop : -0.93 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 597 HIS 0.012 0.001 HIS C 549 PHE 0.020 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.008 0.000 ARG F 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9043 (tttp) cc_final: 0.8704 (ttpt) REVERT: D 73 ASP cc_start: 0.8734 (t0) cc_final: 0.7951 (t0) REVERT: A 140 LYS cc_start: 0.8841 (mttm) cc_final: 0.8446 (mttp) REVERT: C 184 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8971 (pp) REVERT: E 65 LYS cc_start: 0.9097 (tttp) cc_final: 0.8830 (ttpt) REVERT: F 6 GLU cc_start: 0.8718 (mp0) cc_final: 0.8295 (mp0) REVERT: F 118 GLN cc_start: 0.9068 (tp40) cc_final: 0.8690 (tp40) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.2828 time to fit residues: 49.8092 Evaluate side-chains 136 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 HIS C 549 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10110 Z= 0.258 Angle : 0.597 7.053 13725 Z= 0.296 Chirality : 0.045 0.197 1547 Planarity : 0.004 0.041 1755 Dihedral : 13.500 127.788 1773 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.58 % Favored : 95.02 % Rotamer: Outliers : 1.39 % Allowed : 11.90 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1224 helix: 2.19 (0.50), residues: 138 sheet: -0.29 (0.25), residues: 366 loop : -0.93 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 597 HIS 0.011 0.001 HIS C 549 PHE 0.019 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.008 0.000 ARG F 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9042 (tttp) cc_final: 0.8705 (ttpt) REVERT: D 73 ASP cc_start: 0.8743 (t0) cc_final: 0.7956 (t0) REVERT: A 140 LYS cc_start: 0.8856 (mttm) cc_final: 0.8467 (mttp) REVERT: C 184 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8981 (pp) REVERT: E 5 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8377 (tp40) REVERT: E 65 LYS cc_start: 0.9089 (tttp) cc_final: 0.8821 (ttpt) REVERT: F 6 GLU cc_start: 0.8701 (mp0) cc_final: 0.8283 (mp0) REVERT: F 118 GLN cc_start: 0.9051 (tp40) cc_final: 0.8670 (tp40) outliers start: 14 outliers final: 12 residues processed: 133 average time/residue: 0.2862 time to fit residues: 50.8745 Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 112 optimal weight: 0.0570 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.0070 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 HIS C 549 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10110 Z= 0.167 Angle : 0.570 6.931 13725 Z= 0.283 Chirality : 0.043 0.189 1547 Planarity : 0.004 0.045 1755 Dihedral : 13.063 128.327 1773 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.41 % Favored : 95.26 % Rotamer: Outliers : 1.29 % Allowed : 11.81 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1224 helix: 2.16 (0.50), residues: 138 sheet: -0.16 (0.24), residues: 387 loop : -0.92 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 597 HIS 0.013 0.001 HIS B 549 PHE 0.016 0.001 PHE A 193 TYR 0.024 0.001 TYR A 162 ARG 0.008 0.000 ARG F 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9027 (tttp) cc_final: 0.8694 (ttpt) REVERT: D 73 ASP cc_start: 0.8731 (t0) cc_final: 0.8082 (t0) REVERT: A 140 LYS cc_start: 0.8834 (mttm) cc_final: 0.8456 (mttp) REVERT: E 65 LYS cc_start: 0.9067 (tttp) cc_final: 0.8798 (ttpt) REVERT: E 89 GLU cc_start: 0.9246 (pm20) cc_final: 0.9017 (pm20) REVERT: F 6 GLU cc_start: 0.8678 (mp0) cc_final: 0.8270 (mp0) REVERT: F 118 GLN cc_start: 0.8987 (tp40) cc_final: 0.8608 (tp40) outliers start: 13 outliers final: 12 residues processed: 135 average time/residue: 0.2844 time to fit residues: 51.2431 Evaluate side-chains 136 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 100 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 549 HIS C 549 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.063862 restraints weight = 16068.574| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 3.13 r_work: 0.2541 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10110 Z= 0.160 Angle : 0.559 7.059 13725 Z= 0.278 Chirality : 0.043 0.181 1547 Planarity : 0.004 0.047 1755 Dihedral : 12.747 128.089 1773 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.58 % Favored : 95.10 % Rotamer: Outliers : 1.19 % Allowed : 11.90 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1224 helix: 2.12 (0.50), residues: 138 sheet: -0.12 (0.24), residues: 387 loop : -0.89 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 597 HIS 0.012 0.001 HIS B 549 PHE 0.015 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.007 0.000 ARG F 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.89 seconds wall clock time: 40 minutes 54.68 seconds (2454.68 seconds total)