Starting phenix.real_space_refine on Wed Apr 30 21:14:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsv_44873/04_2025/9bsv_44873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsv_44873/04_2025/9bsv_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_44873/04_2025/9bsv_44873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsv_44873/04_2025/9bsv_44873.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsv_44873/04_2025/9bsv_44873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsv_44873/04_2025/9bsv_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-5669/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: 6.25, per 1000 atoms: 0.63 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: 2.67 Conformation dependent library (CDL) restraints added in 1.1 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: 1.30 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: 2.71 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 24.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- 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 : 0.006 0.341 10148 Z= 0.427 Angle : 0.786 13.390 13819 Z= 0.403 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 Details of bonding type rmsd link_NAG-ASN : bond 0.02703 ( 3) link_NAG-ASN : angle 5.73713 ( 9) link_ALPHA1-4 : bond 0.04617 ( 2) link_ALPHA1-4 : angle 7.02811 ( 6) link_ALPHA1-6 : bond 0.03759 ( 4) link_ALPHA1-6 : angle 3.48621 ( 12) link_BETA1-4 : bond 0.04805 ( 5) link_BETA1-4 : angle 5.70375 ( 15) link_ALPHA1-2 : bond 0.04565 ( 1) link_ALPHA1-2 : angle 4.95586 ( 3) link_ALPHA1-3 : bond 0.04670 ( 4) link_ALPHA1-3 : angle 5.08417 ( 12) hydrogen bonds : bond 0.22207 ( 264) hydrogen bonds : angle 8.90121 ( 741) link_BETA1-6 : bond 0.03197 ( 1) link_BETA1-6 : angle 4.42600 ( 3) SS BOND : bond 0.00269 ( 17) SS BOND : angle 1.08303 ( 34) covalent geometry : bond 0.00452 (10110) covalent geometry : angle 0.70506 (13725) Misc. bond : bond 0.34128 ( 1) *********************** 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 : 1.104 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: 0.3221 time to fit residues: 72.8480 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 : 1.014 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.063328 restraints weight = 16289.033| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 3.07 r_work: 0.2513 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 10148 Z= 0.195 Angle : 0.682 8.121 13819 Z= 0.331 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 3) link_NAG-ASN : angle 3.37360 ( 9) link_ALPHA1-4 : bond 0.01508 ( 2) link_ALPHA1-4 : angle 4.16372 ( 6) link_ALPHA1-6 : bond 0.01338 ( 4) link_ALPHA1-6 : angle 2.22354 ( 12) link_BETA1-4 : bond 0.00166 ( 5) link_BETA1-4 : angle 2.81032 ( 15) link_ALPHA1-2 : bond 0.01604 ( 1) link_ALPHA1-2 : angle 2.24562 ( 3) link_ALPHA1-3 : bond 0.00629 ( 4) link_ALPHA1-3 : angle 3.31047 ( 12) hydrogen bonds : bond 0.04902 ( 264) hydrogen bonds : angle 5.75311 ( 741) link_BETA1-6 : bond 0.01501 ( 1) link_BETA1-6 : angle 3.33979 ( 3) SS BOND : bond 0.00343 ( 17) SS BOND : angle 1.35568 ( 34) covalent geometry : bond 0.00464 (10110) covalent geometry : angle 0.65041 (13725) Misc. bond : bond 0.00342 ( 1) *********************** 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 : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8949 (tttp) cc_final: 0.8627 (ttmt) REVERT: D 73 ASP cc_start: 0.8409 (t0) cc_final: 0.7717 (t0) REVERT: D 105 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8338 (m-40) REVERT: A 140 LYS cc_start: 0.8516 (mttm) cc_final: 0.8107 (mttp) REVERT: B 44 GLN cc_start: 0.8237 (mt0) cc_final: 0.8030 (mt0) REVERT: E 3 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8520 (mp10) REVERT: E 65 LYS cc_start: 0.8992 (tttp) cc_final: 0.8708 (ttpt) REVERT: F 6 GLU cc_start: 0.8711 (mp0) cc_final: 0.8473 (mp0) outliers start: 12 outliers final: 10 residues processed: 136 average time/residue: 0.3094 time to fit residues: 54.8696 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 : 1.006 ------------------------------------------------------------------------------- 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 117 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.062691 restraints weight = 16450.274| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.13 r_work: 0.2523 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10148 Z= 0.149 Angle : 0.624 7.909 13819 Z= 0.302 Chirality : 0.044 0.219 1547 Planarity : 0.004 0.041 1755 Dihedral : 15.976 130.994 1773 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.08 % Favored : 95.51 % Rotamer: Outliers : 1.59 % Allowed : 8.13 % Favored : 90.28 % 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: -0.61 (0.23), residues: 1224 helix: 2.17 (0.49), residues: 138 sheet: -0.32 (0.24), residues: 387 loop : -0.98 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 597 HIS 0.009 0.001 HIS B 549 PHE 0.019 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.005 0.000 ARG D 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 3) link_NAG-ASN : angle 2.79198 ( 9) link_ALPHA1-4 : bond 0.01498 ( 2) link_ALPHA1-4 : angle 4.13915 ( 6) link_ALPHA1-6 : bond 0.01418 ( 4) link_ALPHA1-6 : angle 2.43221 ( 12) link_BETA1-4 : bond 0.00224 ( 5) link_BETA1-4 : angle 2.73779 ( 15) link_ALPHA1-2 : bond 0.02335 ( 1) link_ALPHA1-2 : angle 2.31645 ( 3) link_ALPHA1-3 : bond 0.00458 ( 4) link_ALPHA1-3 : angle 3.24536 ( 12) hydrogen bonds : bond 0.04392 ( 264) hydrogen bonds : angle 5.18889 ( 741) link_BETA1-6 : bond 0.01304 ( 1) link_BETA1-6 : angle 3.96215 ( 3) SS BOND : bond 0.00211 ( 17) SS BOND : angle 1.23190 ( 34) covalent geometry : bond 0.00346 (10110) covalent geometry : angle 0.59007 (13725) Misc. bond : bond 0.00059 ( 1) *********************** 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 141 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8942 (tttp) cc_final: 0.8620 (ttpt) REVERT: D 73 ASP cc_start: 0.8431 (t0) cc_final: 0.7697 (t0) REVERT: A 140 LYS cc_start: 0.8514 (mttm) cc_final: 0.8112 (mttp) REVERT: A 597 TRP cc_start: 0.6601 (m-90) cc_final: 0.6323 (m-90) REVERT: B 44 GLN cc_start: 0.8265 (mt0) cc_final: 0.8064 (mt0) REVERT: E 65 LYS cc_start: 0.8982 (tttp) cc_final: 0.8698 (ttpt) REVERT: E 120 THR cc_start: 0.9054 (m) cc_final: 0.8712 (p) REVERT: F 6 GLU cc_start: 0.8682 (mp0) cc_final: 0.8344 (mp0) REVERT: F 57 ARG cc_start: 0.8592 (tpt90) cc_final: 0.8218 (tpt-90) outliers start: 16 outliers final: 13 residues processed: 135 average time/residue: 0.2883 time to fit residues: 51.1813 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 : 0.996 ------------------------------------------------------------------------------- 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 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 76 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.062403 restraints weight = 16287.089| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 2.77 r_work: 0.2497 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2336 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10148 Z= 0.219 Angle : 0.647 8.948 13819 Z= 0.315 Chirality : 0.045 0.210 1547 Planarity : 0.004 0.039 1755 Dihedral : 15.337 129.852 1773 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.41 % Favored : 95.10 % Rotamer: Outliers : 1.59 % Allowed : 8.93 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.28 (0.49), residues: 138 sheet: -0.27 (0.24), residues: 402 loop : -1.02 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 101 HIS 0.004 0.001 HIS B 549 PHE 0.022 0.002 PHE A 193 TYR 0.024 0.001 TYR A 162 ARG 0.005 0.000 ARG D 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 3) link_NAG-ASN : angle 2.65917 ( 9) link_ALPHA1-4 : bond 0.01523 ( 2) link_ALPHA1-4 : angle 4.48113 ( 6) link_ALPHA1-6 : bond 0.01352 ( 4) link_ALPHA1-6 : angle 2.73256 ( 12) link_BETA1-4 : bond 0.00189 ( 5) link_BETA1-4 : angle 2.99106 ( 15) link_ALPHA1-2 : bond 0.02570 ( 1) link_ALPHA1-2 : angle 2.91782 ( 3) link_ALPHA1-3 : bond 0.00359 ( 4) link_ALPHA1-3 : angle 3.07417 ( 12) hydrogen bonds : bond 0.04520 ( 264) hydrogen bonds : angle 4.97246 ( 741) link_BETA1-6 : bond 0.01042 ( 1) link_BETA1-6 : angle 4.28855 ( 3) SS BOND : bond 0.00277 ( 17) SS BOND : angle 1.38005 ( 34) covalent geometry : bond 0.00530 (10110) covalent geometry : angle 0.61023 (13725) Misc. bond : bond 0.00017 ( 1) *********************** 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 136 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9313 (tttp) cc_final: 0.9082 (ttmt) REVERT: D 73 ASP cc_start: 0.9198 (t0) cc_final: 0.8556 (t0) REVERT: A 140 LYS cc_start: 0.9066 (mttm) cc_final: 0.8707 (mttp) REVERT: E 120 THR cc_start: 0.9285 (m) cc_final: 0.9031 (p) REVERT: F 6 GLU cc_start: 0.8998 (mp0) cc_final: 0.8630 (mp0) outliers start: 16 outliers final: 14 residues processed: 128 average time/residue: 0.2945 time to fit residues: 49.6666 Evaluate side-chains 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 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 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS C 549 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.062162 restraints weight = 16214.159| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 3.12 r_work: 0.2507 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10148 Z= 0.144 Angle : 0.610 8.819 13819 Z= 0.295 Chirality : 0.044 0.228 1547 Planarity : 0.004 0.043 1755 Dihedral : 14.748 127.760 1773 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.00 % Favored : 95.59 % Rotamer: Outliers : 1.79 % Allowed : 9.62 % Favored : 88.59 % 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: 2.23 (0.49), residues: 138 sheet: -0.27 (0.24), residues: 387 loop : -0.98 (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 0.019 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.003 0.000 ARG D 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 3) link_NAG-ASN : angle 2.43227 ( 9) link_ALPHA1-4 : bond 0.01584 ( 2) link_ALPHA1-4 : angle 4.09687 ( 6) link_ALPHA1-6 : bond 0.01415 ( 4) link_ALPHA1-6 : angle 2.64759 ( 12) link_BETA1-4 : bond 0.00233 ( 5) link_BETA1-4 : angle 2.82452 ( 15) link_ALPHA1-2 : bond 0.02384 ( 1) link_ALPHA1-2 : angle 3.00835 ( 3) link_ALPHA1-3 : bond 0.00351 ( 4) link_ALPHA1-3 : angle 3.07946 ( 12) hydrogen bonds : bond 0.04042 ( 264) hydrogen bonds : angle 4.78643 ( 741) link_BETA1-6 : bond 0.01084 ( 1) link_BETA1-6 : angle 4.27448 ( 3) SS BOND : bond 0.00243 ( 17) SS BOND : angle 1.15254 ( 34) covalent geometry : bond 0.00337 (10110) covalent geometry : angle 0.57522 (13725) Misc. bond : bond 0.00012 ( 1) *********************** 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: 18 poor density : 126 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 6 GLU cc_start: 0.8653 (mp0) cc_final: 0.8452 (mp0) REVERT: D 65 LYS cc_start: 0.8929 (tttp) cc_final: 0.8609 (ttpt) REVERT: D 73 ASP cc_start: 0.8506 (t0) cc_final: 0.7746 (t0) REVERT: A 140 LYS cc_start: 0.8555 (mttm) cc_final: 0.8161 (mttp) REVERT: C 184 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8463 (pp) REVERT: E 120 THR cc_start: 0.9050 (m) cc_final: 0.8758 (p) REVERT: F 6 GLU cc_start: 0.8591 (mp0) cc_final: 0.8227 (mp0) outliers start: 18 outliers final: 13 residues processed: 137 average time/residue: 0.2955 time to fit residues: 53.7940 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 : 1.004 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 94 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.064100 restraints weight = 16306.378| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 3.11 r_work: 0.2531 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10148 Z= 0.117 Angle : 0.595 8.704 13819 Z= 0.285 Chirality : 0.043 0.235 1547 Planarity : 0.004 0.039 1755 Dihedral : 14.188 126.460 1773 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.92 % Favored : 95.67 % Rotamer: Outliers : 1.69 % Allowed : 10.91 % Favored : 87.40 % 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: -0.52 (0.23), residues: 1224 helix: 2.24 (0.49), residues: 138 sheet: -0.22 (0.24), residues: 387 loop : -0.95 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 597 HIS 0.020 0.001 HIS B 549 PHE 0.017 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.005 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 3) link_NAG-ASN : angle 2.23582 ( 9) link_ALPHA1-4 : bond 0.01571 ( 2) link_ALPHA1-4 : angle 3.90311 ( 6) link_ALPHA1-6 : bond 0.01482 ( 4) link_ALPHA1-6 : angle 2.48166 ( 12) link_BETA1-4 : bond 0.00303 ( 5) link_BETA1-4 : angle 2.73170 ( 15) link_ALPHA1-2 : bond 0.02323 ( 1) link_ALPHA1-2 : angle 3.01523 ( 3) link_ALPHA1-3 : bond 0.00368 ( 4) link_ALPHA1-3 : angle 3.05309 ( 12) hydrogen bonds : bond 0.03693 ( 264) hydrogen bonds : angle 4.62727 ( 741) link_BETA1-6 : bond 0.01062 ( 1) link_BETA1-6 : angle 4.38490 ( 3) SS BOND : bond 0.00155 ( 17) SS BOND : angle 1.06422 ( 34) covalent geometry : bond 0.00264 (10110) covalent geometry : angle 0.56162 (13725) Misc. bond : bond 0.00004 ( 1) *********************** 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 141 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8961 (tttp) cc_final: 0.8642 (ttpt) REVERT: D 73 ASP cc_start: 0.8586 (t0) cc_final: 0.7802 (t0) REVERT: A 140 LYS cc_start: 0.8630 (mttm) cc_final: 0.8234 (mttp) REVERT: A 597 TRP cc_start: 0.6526 (m-90) cc_final: 0.6280 (m-90) REVERT: C 184 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8562 (pp) REVERT: E 120 THR cc_start: 0.9093 (m) cc_final: 0.8829 (p) REVERT: F 6 GLU cc_start: 0.8652 (mp0) cc_final: 0.8225 (mp0) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.2782 time to fit residues: 49.8896 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 : 1.089 ------------------------------------------------------------------------------- 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 A residue 595 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.063864 restraints weight = 16471.779| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 3.11 r_work: 0.2519 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10148 Z= 0.136 Angle : 0.610 8.415 13819 Z= 0.292 Chirality : 0.044 0.223 1547 Planarity : 0.004 0.043 1755 Dihedral : 13.781 125.826 1773 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.00 % Favored : 95.59 % Rotamer: Outliers : 1.39 % Allowed : 11.31 % 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: -0.49 (0.23), residues: 1224 helix: 2.25 (0.50), residues: 138 sheet: -0.20 (0.24), residues: 387 loop : -0.92 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 597 HIS 0.017 0.001 HIS B 549 PHE 0.017 0.001 PHE A 193 TYR 0.022 0.001 TYR A 162 ARG 0.006 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 3) link_NAG-ASN : angle 2.18352 ( 9) link_ALPHA1-4 : bond 0.01558 ( 2) link_ALPHA1-4 : angle 4.03620 ( 6) link_ALPHA1-6 : bond 0.01410 ( 4) link_ALPHA1-6 : angle 2.57104 ( 12) link_BETA1-4 : bond 0.00254 ( 5) link_BETA1-4 : angle 2.78743 ( 15) link_ALPHA1-2 : bond 0.02391 ( 1) link_ALPHA1-2 : angle 3.04788 ( 3) link_ALPHA1-3 : bond 0.00375 ( 4) link_ALPHA1-3 : angle 2.99247 ( 12) hydrogen bonds : bond 0.03745 ( 264) hydrogen bonds : angle 4.53773 ( 741) link_BETA1-6 : bond 0.00935 ( 1) link_BETA1-6 : angle 4.80080 ( 3) SS BOND : bond 0.00237 ( 17) SS BOND : angle 1.51279 ( 34) covalent geometry : bond 0.00320 (10110) covalent geometry : angle 0.57434 (13725) Misc. bond : bond 0.00006 ( 1) *********************** 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: 14 poor density : 124 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8922 (tttp) cc_final: 0.8588 (ttpt) REVERT: D 73 ASP cc_start: 0.8522 (t0) cc_final: 0.7735 (t0) REVERT: A 140 LYS cc_start: 0.8575 (mttm) cc_final: 0.8177 (mttp) REVERT: C 184 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8502 (pp) REVERT: E 120 THR cc_start: 0.9056 (m) cc_final: 0.8802 (p) REVERT: F 6 GLU cc_start: 0.8631 (mp0) cc_final: 0.8174 (mp0) REVERT: F 118 GLN cc_start: 0.8843 (tp40) cc_final: 0.8460 (tp40) outliers start: 14 outliers final: 12 residues processed: 134 average time/residue: 0.2781 time to fit residues: 49.9278 Evaluate side-chains 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER 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 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 116 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 81 optimal weight: 0.0070 chunk 99 optimal weight: 5.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.062832 restraints weight = 16418.434| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.15 r_work: 0.2520 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10148 Z= 0.136 Angle : 0.611 7.789 13819 Z= 0.292 Chirality : 0.044 0.207 1547 Planarity : 0.004 0.041 1755 Dihedral : 13.398 125.741 1773 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.08 % Favored : 95.51 % Rotamer: Outliers : 1.39 % Allowed : 11.61 % Favored : 87.00 % 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: -0.46 (0.23), residues: 1224 helix: 2.26 (0.50), residues: 138 sheet: -0.17 (0.24), residues: 387 loop : -0.90 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 597 HIS 0.015 0.001 HIS B 549 PHE 0.017 0.001 PHE A 193 TYR 0.022 0.001 TYR A 162 ARG 0.005 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 3) link_NAG-ASN : angle 2.15544 ( 9) link_ALPHA1-4 : bond 0.01570 ( 2) link_ALPHA1-4 : angle 4.07766 ( 6) link_ALPHA1-6 : bond 0.01395 ( 4) link_ALPHA1-6 : angle 2.61681 ( 12) link_BETA1-4 : bond 0.00257 ( 5) link_BETA1-4 : angle 2.79699 ( 15) link_ALPHA1-2 : bond 0.02380 ( 1) link_ALPHA1-2 : angle 2.99004 ( 3) link_ALPHA1-3 : bond 0.00382 ( 4) link_ALPHA1-3 : angle 2.99297 ( 12) hydrogen bonds : bond 0.03740 ( 264) hydrogen bonds : angle 4.49710 ( 741) link_BETA1-6 : bond 0.00677 ( 1) link_BETA1-6 : angle 5.10455 ( 3) SS BOND : bond 0.00217 ( 17) SS BOND : angle 1.31544 ( 34) covalent geometry : bond 0.00318 (10110) covalent geometry : angle 0.57591 (13725) Misc. bond : bond 0.00007 ( 1) *********************** 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 143 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8917 (tttp) cc_final: 0.8579 (ttpt) REVERT: D 73 ASP cc_start: 0.8541 (t0) cc_final: 0.7766 (t0) REVERT: A 140 LYS cc_start: 0.8584 (mttm) cc_final: 0.8187 (mttp) REVERT: C 184 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8525 (pp) REVERT: E 5 GLN cc_start: 0.8521 (tp40) cc_final: 0.8288 (tp-100) REVERT: F 6 GLU cc_start: 0.8603 (mp0) cc_final: 0.8136 (mp0) REVERT: F 118 GLN cc_start: 0.8755 (tp40) cc_final: 0.8369 (tp40) outliers start: 14 outliers final: 12 residues processed: 139 average time/residue: 0.3129 time to fit residues: 57.5630 Evaluate side-chains 137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER 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 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 46 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 0.0170 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.062538 restraints weight = 16471.311| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.12 r_work: 0.2492 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10148 Z= 0.187 Angle : 0.638 8.480 13819 Z= 0.307 Chirality : 0.045 0.187 1547 Planarity : 0.004 0.042 1755 Dihedral : 13.266 126.486 1773 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.66 % Favored : 94.93 % Rotamer: Outliers : 1.39 % Allowed : 11.81 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.23), residues: 1224 helix: 2.26 (0.50), residues: 138 sheet: -0.18 (0.24), residues: 387 loop : -0.96 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 597 HIS 0.023 0.001 HIS B 549 PHE 0.020 0.001 PHE A 193 TYR 0.022 0.001 TYR A 162 ARG 0.005 0.000 ARG B 596 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 3) link_NAG-ASN : angle 2.22717 ( 9) link_ALPHA1-4 : bond 0.01580 ( 2) link_ALPHA1-4 : angle 4.42078 ( 6) link_ALPHA1-6 : bond 0.01382 ( 4) link_ALPHA1-6 : angle 2.91191 ( 12) link_BETA1-4 : bond 0.00177 ( 5) link_BETA1-4 : angle 2.94758 ( 15) link_ALPHA1-2 : bond 0.02319 ( 1) link_ALPHA1-2 : angle 3.03183 ( 3) link_ALPHA1-3 : bond 0.00332 ( 4) link_ALPHA1-3 : angle 2.95029 ( 12) hydrogen bonds : bond 0.04093 ( 264) hydrogen bonds : angle 4.53288 ( 741) link_BETA1-6 : bond 0.00202 ( 1) link_BETA1-6 : angle 5.18083 ( 3) SS BOND : bond 0.00247 ( 17) SS BOND : angle 1.42986 ( 34) covalent geometry : bond 0.00449 (10110) covalent geometry : angle 0.60081 (13725) Misc. bond : bond 0.00014 ( 1) *********************** 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 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8928 (tttp) cc_final: 0.8584 (ttpt) REVERT: D 73 ASP cc_start: 0.8569 (t0) cc_final: 0.7765 (t0) REVERT: A 140 LYS cc_start: 0.8579 (mttm) cc_final: 0.8183 (mttp) REVERT: A 597 TRP cc_start: 0.6517 (m-90) cc_final: 0.6304 (m-90) REVERT: C 184 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8492 (pp) REVERT: E 120 THR cc_start: 0.9076 (m) cc_final: 0.8831 (p) REVERT: F 6 GLU cc_start: 0.8602 (mp0) cc_final: 0.8181 (mp0) REVERT: F 118 GLN cc_start: 0.8764 (tp40) cc_final: 0.8370 (tp40) outliers start: 14 outliers final: 12 residues processed: 130 average time/residue: 0.3296 time to fit residues: 58.1462 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 : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP 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 196 SER Chi-restraints excluded: chain C residue 504 ILE 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 103 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 chunk 40 optimal weight: 0.0010 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.063149 restraints weight = 16194.782| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 3.14 r_work: 0.2525 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10148 Z= 0.116 Angle : 0.600 7.285 13819 Z= 0.289 Chirality : 0.043 0.181 1547 Planarity : 0.004 0.042 1755 Dihedral : 12.843 127.255 1773 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.33 % Favored : 95.34 % 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: 2.23 (0.50), residues: 138 sheet: -0.14 (0.24), residues: 387 loop : -0.90 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 597 HIS 0.018 0.001 HIS B 549 PHE 0.015 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.009 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 3) link_NAG-ASN : angle 2.13541 ( 9) link_ALPHA1-4 : bond 0.01560 ( 2) link_ALPHA1-4 : angle 4.05258 ( 6) link_ALPHA1-6 : bond 0.01386 ( 4) link_ALPHA1-6 : angle 2.74052 ( 12) link_BETA1-4 : bond 0.00317 ( 5) link_BETA1-4 : angle 2.77875 ( 15) link_ALPHA1-2 : bond 0.02317 ( 1) link_ALPHA1-2 : angle 2.81757 ( 3) link_ALPHA1-3 : bond 0.00422 ( 4) link_ALPHA1-3 : angle 3.05067 ( 12) hydrogen bonds : bond 0.03600 ( 264) hydrogen bonds : angle 4.45885 ( 741) link_BETA1-6 : bond 0.00167 ( 1) link_BETA1-6 : angle 4.23411 ( 3) SS BOND : bond 0.00190 ( 17) SS BOND : angle 1.11992 ( 34) covalent geometry : bond 0.00264 (10110) covalent geometry : angle 0.56636 (13725) Misc. bond : bond 0.00007 ( 1) ********************** 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 137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8919 (tttp) cc_final: 0.8582 (ttpt) REVERT: D 73 ASP cc_start: 0.8551 (t0) cc_final: 0.7884 (t0) REVERT: A 140 LYS cc_start: 0.8569 (mttm) cc_final: 0.8195 (mttp) REVERT: C 184 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8505 (pp) REVERT: E 89 GLU cc_start: 0.9290 (pm20) cc_final: 0.9031 (pm20) REVERT: E 120 THR cc_start: 0.9078 (m) cc_final: 0.8859 (p) REVERT: F 6 GLU cc_start: 0.8568 (mp0) cc_final: 0.8110 (mp0) REVERT: F 118 GLN cc_start: 0.8722 (tp40) cc_final: 0.8334 (tp40) outliers start: 12 outliers final: 11 residues processed: 135 average time/residue: 0.2698 time to fit residues: 48.4362 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 : 0.993 ------------------------------------------------------------------------------- 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 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 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.063724 restraints weight = 16310.953| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 3.15 r_work: 0.2536 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10148 Z= 0.111 Angle : 0.589 7.177 13819 Z= 0.284 Chirality : 0.043 0.182 1547 Planarity : 0.004 0.046 1755 Dihedral : 12.568 126.995 1773 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.18 % Rotamer: Outliers : 1.19 % Allowed : 12.20 % Favored : 86.61 % 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: -0.41 (0.23), residues: 1224 helix: 2.23 (0.50), residues: 138 sheet: -0.12 (0.24), residues: 387 loop : -0.86 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 597 HIS 0.020 0.001 HIS B 549 PHE 0.015 0.001 PHE A 193 TYR 0.022 0.001 TYR A 162 ARG 0.009 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 3) link_NAG-ASN : angle 2.06456 ( 9) link_ALPHA1-4 : bond 0.01465 ( 2) link_ALPHA1-4 : angle 3.96328 ( 6) link_ALPHA1-6 : bond 0.01373 ( 4) link_ALPHA1-6 : angle 2.69537 ( 12) link_BETA1-4 : bond 0.00342 ( 5) link_BETA1-4 : angle 2.74594 ( 15) link_ALPHA1-2 : bond 0.02327 ( 1) link_ALPHA1-2 : angle 2.87740 ( 3) link_ALPHA1-3 : bond 0.00474 ( 4) link_ALPHA1-3 : angle 3.02090 ( 12) hydrogen bonds : bond 0.03479 ( 264) hydrogen bonds : angle 4.38503 ( 741) link_BETA1-6 : bond 0.00153 ( 1) link_BETA1-6 : angle 3.24768 ( 3) SS BOND : bond 0.00184 ( 17) SS BOND : angle 1.09839 ( 34) covalent geometry : bond 0.00250 (10110) covalent geometry : angle 0.55659 (13725) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4630.01 seconds wall clock time: 81 minutes 20.17 seconds (4880.17 seconds total)