Starting phenix.real_space_refine on Tue May 13 08:49:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsv_44873/05_2025/9bsv_44873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsv_44873/05_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_44873/05_2025/9bsv_44873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsv_44873/05_2025/9bsv_44873.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsv_44873/05_2025/9bsv_44873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsv_44873/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.81, per 1000 atoms: 0.69 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: 2.66 Conformation dependent library (CDL) restraints added in 993.6 milliseconds 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: 1.17 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: 2.88 Time building geometry restraints manager: 2.99 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: 1.610 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.830 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- 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 : 1.089 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: 0.3355 time to fit residues: 75.9351 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 : 0.993 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.063337 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: 0.8432 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 : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8948 (tttp) cc_final: 0.8626 (ttmt) REVERT: D 73 ASP cc_start: 0.8407 (t0) cc_final: 0.7716 (t0) REVERT: D 105 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8337 (m-40) REVERT: A 140 LYS cc_start: 0.8512 (mttm) cc_final: 0.8103 (mttp) REVERT: B 44 GLN cc_start: 0.8235 (mt0) cc_final: 0.8028 (mt0) REVERT: E 3 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8520 (mp10) REVERT: E 65 LYS cc_start: 0.8991 (tttp) cc_final: 0.8707 (ttpt) REVERT: F 6 GLU cc_start: 0.8710 (mp0) cc_final: 0.8473 (mp0) outliers start: 12 outliers final: 10 residues processed: 136 average time/residue: 0.3487 time to fit residues: 62.5268 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 : 1.099 ------------------------------------------------------------------------------- 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: 0.0770 chunk 2 optimal weight: 0.3980 chunk 122 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.096910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.063068 restraints weight = 16425.629| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.12 r_work: 0.2528 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1330 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= 0.138 Angle : 0.618 7.720 13819 Z= 0.299 Chirality : 0.044 0.222 1547 Planarity : 0.004 0.042 1755 Dihedral : 15.991 130.690 1773 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.00 % Favored : 95.59 % Rotamer: Outliers : 1.49 % Allowed : 8.23 % 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: -0.60 (0.23), residues: 1224 helix: 2.17 (0.49), residues: 138 sheet: -0.31 (0.24), residues: 387 loop : -0.97 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 597 HIS 0.011 0.001 HIS B 549 PHE 0.018 0.001 PHE A 193 TYR 0.023 0.001 TYR A 162 ARG 0.005 0.000 ARG D 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 3) link_NAG-ASN : angle 2.77890 ( 9) link_ALPHA1-4 : bond 0.01498 ( 2) link_ALPHA1-4 : angle 4.08545 ( 6) link_ALPHA1-6 : bond 0.01431 ( 4) link_ALPHA1-6 : angle 2.37415 ( 12) link_BETA1-4 : bond 0.00253 ( 5) link_BETA1-4 : angle 2.70662 ( 15) link_ALPHA1-2 : bond 0.02082 ( 1) link_ALPHA1-2 : angle 2.26262 ( 3) link_ALPHA1-3 : bond 0.00457 ( 4) link_ALPHA1-3 : angle 3.25453 ( 12) hydrogen bonds : bond 0.04309 ( 264) hydrogen bonds : angle 5.18583 ( 741) link_BETA1-6 : bond 0.01337 ( 1) link_BETA1-6 : angle 3.92952 ( 3) SS BOND : bond 0.00196 ( 17) SS BOND : angle 1.16576 ( 34) covalent geometry : bond 0.00318 (10110) covalent geometry : angle 0.58493 (13725) Misc. bond : bond 0.00024 ( 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: 15 poor density : 126 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8937 (tttp) cc_final: 0.8616 (ttpt) REVERT: D 73 ASP cc_start: 0.8424 (t0) cc_final: 0.7686 (t0) REVERT: A 140 LYS cc_start: 0.8512 (mttm) cc_final: 0.8114 (mttp) REVERT: A 597 TRP cc_start: 0.6596 (m-90) cc_final: 0.6319 (m-90) REVERT: E 65 LYS cc_start: 0.8980 (tttp) cc_final: 0.8700 (ttpt) REVERT: E 120 THR cc_start: 0.9050 (m) cc_final: 0.8708 (p) REVERT: F 6 GLU cc_start: 0.8673 (mp0) cc_final: 0.8389 (mp0) REVERT: F 57 ARG cc_start: 0.8569 (tpt90) cc_final: 0.8226 (tpt-90) outliers start: 15 outliers final: 12 residues processed: 135 average time/residue: 0.2833 time to fit residues: 50.1915 Evaluate side-chains 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 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 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: 0.9980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 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: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 B 550 ASN C 549 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.060539 restraints weight = 16445.563| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 3.02 r_work: 0.2468 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 10148 Z= 0.282 Angle : 0.692 9.901 13819 Z= 0.339 Chirality : 0.047 0.214 1547 Planarity : 0.005 0.039 1755 Dihedral : 15.508 130.219 1773 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.58 % Favored : 94.93 % Rotamer: Outliers : 1.59 % Allowed : 9.52 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.23), residues: 1224 helix: 2.24 (0.50), residues: 138 sheet: -0.30 (0.24), residues: 402 loop : -1.06 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 101 HIS 0.004 0.001 HIS C 549 PHE 0.025 0.002 PHE A 193 TYR 0.026 0.002 TYR A 162 ARG 0.004 0.000 ARG D 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 3) link_NAG-ASN : angle 2.70558 ( 9) link_ALPHA1-4 : bond 0.01597 ( 2) link_ALPHA1-4 : angle 4.85093 ( 6) link_ALPHA1-6 : bond 0.01389 ( 4) link_ALPHA1-6 : angle 2.84539 ( 12) link_BETA1-4 : bond 0.00281 ( 5) link_BETA1-4 : angle 3.13733 ( 15) link_ALPHA1-2 : bond 0.02492 ( 1) link_ALPHA1-2 : angle 3.10992 ( 3) link_ALPHA1-3 : bond 0.00398 ( 4) link_ALPHA1-3 : angle 3.08095 ( 12) hydrogen bonds : bond 0.04981 ( 264) hydrogen bonds : angle 5.04599 ( 741) link_BETA1-6 : bond 0.00955 ( 1) link_BETA1-6 : angle 4.44921 ( 3) SS BOND : bond 0.00309 ( 17) SS BOND : angle 1.67986 ( 34) covalent geometry : bond 0.00685 (10110) covalent geometry : angle 0.65416 (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 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9047 (tttp) cc_final: 0.8705 (ttmt) REVERT: D 73 ASP cc_start: 0.8702 (t0) cc_final: 0.8419 (t0) REVERT: A 140 LYS cc_start: 0.8661 (mttm) cc_final: 0.8258 (mttp) REVERT: A 597 TRP cc_start: 0.6718 (m-90) cc_final: 0.6475 (m-90) REVERT: B 596 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8161 (ttm-80) REVERT: E 65 LYS cc_start: 0.9071 (tttp) cc_final: 0.8779 (ttpt) REVERT: E 120 THR cc_start: 0.9146 (m) cc_final: 0.8811 (p) REVERT: F 6 GLU cc_start: 0.8738 (mp0) cc_final: 0.8366 (mp0) outliers start: 16 outliers final: 15 residues processed: 126 average time/residue: 0.2912 time to fit residues: 47.9987 Evaluate side-chains 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3235 r_free = 0.3235 target = 0.095991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.062002 restraints weight = 16247.840| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 3.12 r_work: 0.2503 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1643 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= 0.141 Angle : 0.615 8.818 13819 Z= 0.298 Chirality : 0.044 0.231 1547 Planarity : 0.004 0.039 1755 Dihedral : 14.763 128.053 1773 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.84 % Favored : 95.75 % Rotamer: Outliers : 1.69 % Allowed : 10.42 % Favored : 87.90 % 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: -0.59 (0.23), residues: 1224 helix: 2.28 (0.50), residues: 138 sheet: -0.28 (0.24), residues: 387 loop : -1.01 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 101 HIS 0.007 0.001 HIS C 549 PHE 0.019 0.001 PHE A 193 TYR 0.024 0.001 TYR A 162 ARG 0.006 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 3) link_NAG-ASN : angle 2.46222 ( 9) link_ALPHA1-4 : bond 0.01668 ( 2) link_ALPHA1-4 : angle 4.11025 ( 6) link_ALPHA1-6 : bond 0.01474 ( 4) link_ALPHA1-6 : angle 2.71273 ( 12) link_BETA1-4 : bond 0.00256 ( 5) link_BETA1-4 : angle 2.85264 ( 15) link_ALPHA1-2 : bond 0.02416 ( 1) link_ALPHA1-2 : angle 2.99069 ( 3) link_ALPHA1-3 : bond 0.00343 ( 4) link_ALPHA1-3 : angle 3.12921 ( 12) hydrogen bonds : bond 0.04023 ( 264) hydrogen bonds : angle 4.80724 ( 741) link_BETA1-6 : bond 0.01101 ( 1) link_BETA1-6 : angle 4.40183 ( 3) SS BOND : bond 0.00254 ( 17) SS BOND : angle 1.08380 ( 34) covalent geometry : bond 0.00324 (10110) covalent geometry : angle 0.58029 (13725) Misc. bond : bond 0.00011 ( 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 141 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8933 (tttp) cc_final: 0.8598 (ttpt) REVERT: D 73 ASP cc_start: 0.8490 (t0) cc_final: 0.7843 (t0) REVERT: A 140 LYS cc_start: 0.8549 (mttm) cc_final: 0.8156 (mttp) REVERT: B 596 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: C 184 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8477 (pp) REVERT: E 65 LYS cc_start: 0.8975 (tttp) cc_final: 0.8687 (ttpt) REVERT: F 6 GLU cc_start: 0.8583 (mp0) cc_final: 0.8138 (mp0) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 0.2648 time to fit residues: 47.3693 Evaluate side-chains 130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 106 optimal weight: 0.0060 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.096609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.062645 restraints weight = 16399.342| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 3.11 r_work: 0.2496 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10148 Z= 0.163 Angle : 0.623 8.655 13819 Z= 0.300 Chirality : 0.044 0.224 1547 Planarity : 0.004 0.038 1755 Dihedral : 14.328 127.401 1773 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.58 % Favored : 95.02 % Rotamer: Outliers : 1.79 % Allowed : 11.31 % 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: -0.58 (0.23), residues: 1224 helix: 2.28 (0.50), residues: 138 sheet: -0.26 (0.24), residues: 387 loop : -1.02 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 597 HIS 0.008 0.001 HIS B 549 PHE 0.019 0.001 PHE A 193 TYR 0.024 0.001 TYR A 162 ARG 0.004 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 3) link_NAG-ASN : angle 2.32110 ( 9) link_ALPHA1-4 : bond 0.01637 ( 2) link_ALPHA1-4 : angle 4.21232 ( 6) link_ALPHA1-6 : bond 0.01426 ( 4) link_ALPHA1-6 : angle 2.73015 ( 12) link_BETA1-4 : bond 0.00195 ( 5) link_BETA1-4 : angle 2.88645 ( 15) link_ALPHA1-2 : bond 0.02340 ( 1) link_ALPHA1-2 : angle 3.08091 ( 3) link_ALPHA1-3 : bond 0.00340 ( 4) link_ALPHA1-3 : angle 3.05151 ( 12) hydrogen bonds : bond 0.04057 ( 264) hydrogen bonds : angle 4.71645 ( 741) link_BETA1-6 : bond 0.00869 ( 1) link_BETA1-6 : angle 4.77448 ( 3) SS BOND : bond 0.00167 ( 17) SS BOND : angle 1.24838 ( 34) covalent geometry : bond 0.00384 (10110) covalent geometry : angle 0.58721 (13725) Misc. bond : bond 0.00011 ( 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 137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8966 (tttp) cc_final: 0.8630 (ttpt) REVERT: D 73 ASP cc_start: 0.8595 (t0) cc_final: 0.7938 (t0) REVERT: A 140 LYS cc_start: 0.8614 (mttm) cc_final: 0.8221 (mttp) REVERT: B 596 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7965 (ttm-80) REVERT: C 184 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8552 (pp) REVERT: E 65 LYS cc_start: 0.9004 (tttp) cc_final: 0.8717 (ttpt) REVERT: F 6 GLU cc_start: 0.8640 (mp0) cc_final: 0.8193 (mp0) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 0.2684 time to fit residues: 46.3787 Evaluate side-chains 130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 508 GLN E 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.059175 restraints weight = 16657.790| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 3.08 r_work: 0.2444 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 10148 Z= 0.288 Angle : 0.720 10.663 13819 Z= 0.349 Chirality : 0.048 0.223 1547 Planarity : 0.005 0.040 1755 Dihedral : 14.304 128.368 1773 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.31 % Favored : 94.20 % Rotamer: Outliers : 1.79 % Allowed : 11.71 % Favored : 86.51 % 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: 2.27 (0.50), residues: 138 sheet: -0.40 (0.24), residues: 381 loop : -1.02 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 597 HIS 0.004 0.001 HIS B 549 PHE 0.027 0.002 PHE A 193 TYR 0.026 0.002 TYR A 162 ARG 0.004 0.000 ARG F 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 3) link_NAG-ASN : angle 2.47599 ( 9) link_ALPHA1-4 : bond 0.01673 ( 2) link_ALPHA1-4 : angle 5.14624 ( 6) link_ALPHA1-6 : bond 0.01297 ( 4) link_ALPHA1-6 : angle 3.19967 ( 12) link_BETA1-4 : bond 0.00327 ( 5) link_BETA1-4 : angle 3.24188 ( 15) link_ALPHA1-2 : bond 0.02283 ( 1) link_ALPHA1-2 : angle 3.19552 ( 3) link_ALPHA1-3 : bond 0.00319 ( 4) link_ALPHA1-3 : angle 3.03950 ( 12) hydrogen bonds : bond 0.04975 ( 264) hydrogen bonds : angle 4.83477 ( 741) link_BETA1-6 : bond 0.00185 ( 1) link_BETA1-6 : angle 5.48721 ( 3) SS BOND : bond 0.00467 ( 17) SS BOND : angle 1.93116 ( 34) covalent geometry : bond 0.00697 (10110) covalent geometry : angle 0.67829 (13725) Misc. bond : bond 0.00026 ( 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 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9044 (tttp) cc_final: 0.8746 (ttpt) REVERT: D 73 ASP cc_start: 0.8682 (t0) cc_final: 0.7899 (t0) REVERT: C 184 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8471 (pp) REVERT: C 547 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7804 (tt) REVERT: E 65 LYS cc_start: 0.9030 (tttp) cc_final: 0.8729 (ttpt) REVERT: F 6 GLU cc_start: 0.8634 (mp0) cc_final: 0.8247 (mp0) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 0.2714 time to fit residues: 44.7748 Evaluate side-chains 127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.062016 restraints weight = 16447.290| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.14 r_work: 0.2501 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1926 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= 0.125 Angle : 0.613 7.920 13819 Z= 0.295 Chirality : 0.044 0.193 1547 Planarity : 0.004 0.042 1755 Dihedral : 13.484 129.880 1773 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.49 % Favored : 95.10 % Rotamer: Outliers : 1.39 % Allowed : 12.30 % Favored : 86.31 % 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: 2.21 (0.50), residues: 138 sheet: -0.26 (0.24), residues: 387 loop : -1.01 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 597 HIS 0.004 0.001 HIS A 516 PHE 0.016 0.001 PHE A 193 TYR 0.024 0.001 TYR A 162 ARG 0.007 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 3) link_NAG-ASN : angle 2.25995 ( 9) link_ALPHA1-4 : bond 0.01673 ( 2) link_ALPHA1-4 : angle 4.11700 ( 6) link_ALPHA1-6 : bond 0.01474 ( 4) link_ALPHA1-6 : angle 2.92041 ( 12) link_BETA1-4 : bond 0.00281 ( 5) link_BETA1-4 : angle 2.90975 ( 15) link_ALPHA1-2 : bond 0.02259 ( 1) link_ALPHA1-2 : angle 2.80088 ( 3) link_ALPHA1-3 : bond 0.00362 ( 4) link_ALPHA1-3 : angle 3.22885 ( 12) hydrogen bonds : bond 0.03719 ( 264) hydrogen bonds : angle 4.63945 ( 741) link_BETA1-6 : bond 0.00207 ( 1) link_BETA1-6 : angle 4.35732 ( 3) SS BOND : bond 0.00255 ( 17) SS BOND : angle 1.20254 ( 34) covalent geometry : bond 0.00287 (10110) covalent geometry : angle 0.57609 (13725) Misc. bond : bond 0.00012 ( 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 137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8925 (tttp) cc_final: 0.8592 (ttpt) REVERT: D 73 ASP cc_start: 0.8528 (t0) cc_final: 0.7866 (t0) REVERT: C 184 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8443 (pp) REVERT: E 65 LYS cc_start: 0.8968 (tttp) cc_final: 0.8676 (ttpt) REVERT: E 89 GLU cc_start: 0.9329 (pm20) cc_final: 0.9083 (pm20) REVERT: F 6 GLU cc_start: 0.8578 (mp0) cc_final: 0.8150 (mp0) REVERT: F 118 GLN cc_start: 0.8810 (tp40) cc_final: 0.8409 (tp40) outliers start: 14 outliers final: 10 residues processed: 134 average time/residue: 0.2758 time to fit residues: 49.6086 Evaluate side-chains 130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 20 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.062723 restraints weight = 16420.302| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.12 r_work: 0.2501 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1981 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= 0.141 Angle : 0.613 7.857 13819 Z= 0.296 Chirality : 0.044 0.185 1547 Planarity : 0.004 0.047 1755 Dihedral : 13.044 128.878 1773 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.49 % Favored : 95.10 % Rotamer: Outliers : 1.39 % Allowed : 12.70 % Favored : 85.91 % 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: -0.55 (0.23), residues: 1224 helix: 2.21 (0.50), residues: 138 sheet: -0.23 (0.24), residues: 387 loop : -0.97 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 597 HIS 0.004 0.001 HIS B 549 PHE 0.018 0.001 PHE A 193 TYR 0.024 0.001 TYR A 162 ARG 0.007 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 3) link_NAG-ASN : angle 2.14610 ( 9) link_ALPHA1-4 : bond 0.01568 ( 2) link_ALPHA1-4 : angle 4.21887 ( 6) link_ALPHA1-6 : bond 0.01378 ( 4) link_ALPHA1-6 : angle 2.93216 ( 12) link_BETA1-4 : bond 0.00237 ( 5) link_BETA1-4 : angle 2.90262 ( 15) link_ALPHA1-2 : bond 0.02429 ( 1) link_ALPHA1-2 : angle 2.88959 ( 3) link_ALPHA1-3 : bond 0.00419 ( 4) link_ALPHA1-3 : angle 3.05519 ( 12) hydrogen bonds : bond 0.03818 ( 264) hydrogen bonds : angle 4.53334 ( 741) link_BETA1-6 : bond 0.00045 ( 1) link_BETA1-6 : angle 3.12559 ( 3) SS BOND : bond 0.00255 ( 17) SS BOND : angle 1.31390 ( 34) covalent geometry : bond 0.00332 (10110) covalent geometry : angle 0.57810 (13725) Misc. bond : bond 0.00011 ( 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 138 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8957 (tttp) cc_final: 0.8621 (ttpt) REVERT: D 73 ASP cc_start: 0.8619 (t0) cc_final: 0.7958 (t0) REVERT: C 184 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8545 (pp) REVERT: E 65 LYS cc_start: 0.8998 (tttp) cc_final: 0.8706 (ttpt) REVERT: F 6 GLU cc_start: 0.8598 (mp0) cc_final: 0.8159 (mp0) REVERT: F 118 GLN cc_start: 0.8813 (tp40) cc_final: 0.8413 (tp40) outliers start: 14 outliers final: 12 residues processed: 136 average time/residue: 0.2570 time to fit residues: 46.5766 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 : 0.990 ------------------------------------------------------------------------------- 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 A residue 595 GLN Chi-restraints excluded: chain B residue 196 SER 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: 3.9990 chunk 105 optimal weight: 0.0010 chunk 23 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 110 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 overall best weight: 1.2326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.061791 restraints weight = 16369.457| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 3.12 r_work: 0.2483 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10148 Z= 0.174 Angle : 0.638 8.262 13819 Z= 0.310 Chirality : 0.045 0.174 1547 Planarity : 0.004 0.046 1755 Dihedral : 12.879 126.109 1773 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.74 % Favored : 94.85 % Rotamer: Outliers : 1.49 % Allowed : 12.30 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1224 helix: 2.18 (0.50), residues: 138 sheet: -0.20 (0.24), residues: 402 loop : -1.02 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 597 HIS 0.004 0.001 HIS C 549 PHE 0.019 0.001 PHE A 193 TYR 0.024 0.001 TYR A 162 ARG 0.009 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 3) link_NAG-ASN : angle 2.25576 ( 9) link_ALPHA1-4 : bond 0.01488 ( 2) link_ALPHA1-4 : angle 4.45581 ( 6) link_ALPHA1-6 : bond 0.01315 ( 4) link_ALPHA1-6 : angle 3.01566 ( 12) link_BETA1-4 : bond 0.00182 ( 5) link_BETA1-4 : angle 2.99107 ( 15) link_ALPHA1-2 : bond 0.02300 ( 1) link_ALPHA1-2 : angle 3.03018 ( 3) link_ALPHA1-3 : bond 0.00371 ( 4) link_ALPHA1-3 : angle 3.05107 ( 12) hydrogen bonds : bond 0.04057 ( 264) hydrogen bonds : angle 4.55345 ( 741) link_BETA1-6 : bond 0.00038 ( 1) link_BETA1-6 : angle 2.51504 ( 3) SS BOND : bond 0.00243 ( 17) SS BOND : angle 1.41355 ( 34) covalent geometry : bond 0.00419 (10110) covalent geometry : angle 0.60321 (13725) Misc. bond : bond 0.00016 ( 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 135 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8966 (tttp) cc_final: 0.8628 (ttpt) REVERT: D 73 ASP cc_start: 0.8647 (t0) cc_final: 0.7993 (t0) REVERT: C 184 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8551 (pp) REVERT: E 5 GLN cc_start: 0.8497 (tp-100) cc_final: 0.8270 (tp40) REVERT: E 65 LYS cc_start: 0.9007 (tttp) cc_final: 0.8711 (ttpt) REVERT: F 6 GLU cc_start: 0.8603 (mp0) cc_final: 0.8207 (mp0) REVERT: F 118 GLN cc_start: 0.8801 (tp40) cc_final: 0.8400 (tp40) outliers start: 15 outliers final: 14 residues processed: 133 average time/residue: 0.2636 time to fit residues: 46.7546 Evaluate side-chains 134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 A residue 595 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.061551 restraints weight = 16402.978| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.15 r_work: 0.2496 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10148 Z= 0.152 Angle : 0.621 7.833 13819 Z= 0.302 Chirality : 0.044 0.177 1547 Planarity : 0.004 0.048 1755 Dihedral : 12.622 124.023 1773 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.41 % Favored : 95.26 % Rotamer: Outliers : 1.39 % Allowed : 12.60 % Favored : 86.01 % 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: -0.55 (0.23), residues: 1224 helix: 2.16 (0.50), residues: 138 sheet: -0.19 (0.24), residues: 402 loop : -1.01 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 597 HIS 0.004 0.001 HIS C 549 PHE 0.017 0.001 PHE A 193 TYR 0.024 0.001 TYR A 162 ARG 0.009 0.000 ARG F 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 3) link_NAG-ASN : angle 2.20135 ( 9) link_ALPHA1-4 : bond 0.01413 ( 2) link_ALPHA1-4 : angle 4.35082 ( 6) link_ALPHA1-6 : bond 0.01305 ( 4) link_ALPHA1-6 : angle 2.92521 ( 12) link_BETA1-4 : bond 0.00207 ( 5) link_BETA1-4 : angle 2.98935 ( 15) link_ALPHA1-2 : bond 0.02290 ( 1) link_ALPHA1-2 : angle 2.87560 ( 3) link_ALPHA1-3 : bond 0.00469 ( 4) link_ALPHA1-3 : angle 3.04782 ( 12) hydrogen bonds : bond 0.03863 ( 264) hydrogen bonds : angle 4.54019 ( 741) link_BETA1-6 : bond 0.00147 ( 1) link_BETA1-6 : angle 2.24038 ( 3) SS BOND : bond 0.00215 ( 17) SS BOND : angle 1.27944 ( 34) covalent geometry : bond 0.00362 (10110) covalent geometry : angle 0.58694 (13725) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4494.43 seconds wall clock time: 78 minutes 41.50 seconds (4721.50 seconds total)