Starting phenix.real_space_refine on Wed Sep 17 17:00:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsv_44873/09_2025/9bsv_44873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsv_44873/09_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_44873/09_2025/9bsv_44873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsv_44873/09_2025/9bsv_44873.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsv_44873/09_2025/9bsv_44873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsv_44873/09_2025/9bsv_44873.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.59, per 1000 atoms: 0.26 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: 1.01 Conformation dependent library (CDL) restraints added in 378.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.38 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: 1.44 Time building geometry restraints manager: 1.33 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.470 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- 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 : 7.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 596 TYR 0.017 0.001 TYR A 162 PHE 0.022 0.001 PHE A 193 TRP 0.018 0.001 TRP A 597 HIS 0.005 0.001 HIS C 549 Details of bonding type rmsd covalent geometry : bond 0.00452 (10110) covalent geometry : angle 0.70506 (13725) SS BOND : bond 0.00269 ( 17) SS BOND : angle 1.08303 ( 34) hydrogen bonds : bond 0.22207 ( 264) hydrogen bonds : angle 8.90121 ( 741) Misc. bond : bond 0.34128 ( 1) 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) 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_BETA1-6 : bond 0.03197 ( 1) link_BETA1-6 : angle 4.42600 ( 3) link_NAG-ASN : bond 0.02703 ( 3) link_NAG-ASN : angle 5.73713 ( 9) *********************** 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 : 0.389 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: 0.1559 time to fit residues: 35.1349 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 : 0.371 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.095117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.061226 restraints weight = 16503.779| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 3.09 r_work: 0.2480 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10148 Z= 0.262 Angle : 0.729 8.539 13819 Z= 0.355 Chirality : 0.049 0.218 1547 Planarity : 0.005 0.050 1755 Dihedral : 18.107 131.161 1773 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.58 % Favored : 94.85 % Rotamer: Outliers : 1.29 % Allowed : 7.54 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.23), residues: 1224 helix: 2.41 (0.50), residues: 120 sheet: -0.45 (0.25), residues: 378 loop : -1.00 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 27 TYR 0.030 0.002 TYR A 162 PHE 0.024 0.002 PHE A 193 TRP 0.018 0.001 TRP F 101 HIS 0.004 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00634 (10110) covalent geometry : angle 0.69600 (13725) SS BOND : bond 0.00354 ( 17) SS BOND : angle 1.55822 ( 34) hydrogen bonds : bond 0.05212 ( 264) hydrogen bonds : angle 5.75409 ( 741) Misc. bond : bond 0.00152 ( 1) link_ALPHA1-2 : bond 0.01385 ( 1) link_ALPHA1-2 : angle 2.49347 ( 3) link_ALPHA1-3 : bond 0.00643 ( 4) link_ALPHA1-3 : angle 3.38940 ( 12) link_ALPHA1-4 : bond 0.01491 ( 2) link_ALPHA1-4 : angle 4.47140 ( 6) link_ALPHA1-6 : bond 0.01362 ( 4) link_ALPHA1-6 : angle 2.37750 ( 12) link_BETA1-4 : bond 0.00269 ( 5) link_BETA1-4 : angle 2.89984 ( 15) link_BETA1-6 : bond 0.01571 ( 1) link_BETA1-6 : angle 3.32734 ( 3) link_NAG-ASN : bond 0.00630 ( 3) link_NAG-ASN : angle 3.32508 ( 9) *********************** 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 137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9042 (tttp) cc_final: 0.8724 (ttmt) REVERT: D 73 ASP cc_start: 0.8530 (t0) cc_final: 0.7805 (t0) REVERT: D 105 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8507 (m-40) REVERT: A 140 LYS cc_start: 0.8572 (mttm) cc_final: 0.8178 (mttp) REVERT: B 44 GLN cc_start: 0.8304 (mt0) cc_final: 0.8083 (mt0) REVERT: B 596 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7997 (ttm-80) REVERT: E 65 LYS cc_start: 0.9030 (tttp) cc_final: 0.8735 (ttpt) REVERT: E 89 GLU cc_start: 0.9086 (pm20) cc_final: 0.8882 (pm20) REVERT: F 57 ARG cc_start: 0.8627 (tpt90) cc_final: 0.8345 (tpt-90) outliers start: 13 outliers final: 11 residues processed: 133 average time/residue: 0.1402 time to fit residues: 24.1891 Evaluate side-chains 125 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 69 THR 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 81 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 E 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.061000 restraints weight = 16599.784| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 3.11 r_work: 0.2471 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10148 Z= 0.235 Angle : 0.677 9.407 13819 Z= 0.330 Chirality : 0.046 0.207 1547 Planarity : 0.005 0.041 1755 Dihedral : 16.156 131.861 1773 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.74 % Favored : 94.69 % Rotamer: Outliers : 1.59 % Allowed : 8.53 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.23), residues: 1224 helix: 2.21 (0.49), residues: 138 sheet: -0.40 (0.24), residues: 402 loop : -1.07 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.025 0.002 TYR A 162 PHE 0.023 0.002 PHE A 193 TRP 0.014 0.001 TRP F 101 HIS 0.008 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00565 (10110) covalent geometry : angle 0.64133 (13725) SS BOND : bond 0.00286 ( 17) SS BOND : angle 1.46539 ( 34) hydrogen bonds : bond 0.04969 ( 264) hydrogen bonds : angle 5.28385 ( 741) Misc. bond : bond 0.00019 ( 1) link_ALPHA1-2 : bond 0.02157 ( 1) link_ALPHA1-2 : angle 2.57430 ( 3) link_ALPHA1-3 : bond 0.00432 ( 4) link_ALPHA1-3 : angle 3.22983 ( 12) link_ALPHA1-4 : bond 0.01548 ( 2) link_ALPHA1-4 : angle 4.68874 ( 6) link_ALPHA1-6 : bond 0.01391 ( 4) link_ALPHA1-6 : angle 2.64492 ( 12) link_BETA1-4 : bond 0.00303 ( 5) link_BETA1-4 : angle 3.05297 ( 15) link_BETA1-6 : bond 0.01237 ( 1) link_BETA1-6 : angle 4.15274 ( 3) link_NAG-ASN : bond 0.00396 ( 3) link_NAG-ASN : angle 2.81740 ( 9) *********************** 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 134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8998 (tttp) cc_final: 0.8674 (ttmt) REVERT: D 73 ASP cc_start: 0.8577 (t0) cc_final: 0.8328 (t0) REVERT: A 140 LYS cc_start: 0.8587 (mttm) cc_final: 0.8182 (mttp) REVERT: B 44 GLN cc_start: 0.8368 (mt0) cc_final: 0.8159 (mt0) REVERT: B 547 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7795 (tt) REVERT: B 597 TRP cc_start: 0.6726 (m-90) cc_final: 0.6502 (m-90) REVERT: E 65 LYS cc_start: 0.9019 (tttp) cc_final: 0.8728 (ttpt) REVERT: E 89 GLU cc_start: 0.9085 (pm20) cc_final: 0.8822 (pm20) REVERT: E 120 THR cc_start: 0.9120 (m) cc_final: 0.8772 (p) REVERT: F 6 GLU cc_start: 0.8773 (mp0) cc_final: 0.8479 (mp0) outliers start: 16 outliers final: 14 residues processed: 127 average time/residue: 0.1341 time to fit residues: 22.5344 Evaluate side-chains 128 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 547 LEU Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 595 GLN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain E residue 69 THR 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 55 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.063637 restraints weight = 16342.767| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.78 r_work: 0.2518 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1595 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= 0.137 Angle : 0.610 8.844 13819 Z= 0.296 Chirality : 0.044 0.230 1547 Planarity : 0.004 0.038 1755 Dihedral : 15.119 128.037 1773 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.92 % Favored : 95.67 % Rotamer: Outliers : 1.88 % Allowed : 9.72 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.23), residues: 1224 helix: 2.23 (0.49), residues: 138 sheet: -0.36 (0.24), residues: 387 loop : -1.00 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.024 0.001 TYR A 162 PHE 0.018 0.001 PHE A 193 TRP 0.013 0.001 TRP A 597 HIS 0.005 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00313 (10110) covalent geometry : angle 0.57546 (13725) SS BOND : bond 0.00255 ( 17) SS BOND : angle 1.17157 ( 34) hydrogen bonds : bond 0.04054 ( 264) hydrogen bonds : angle 4.92765 ( 741) Misc. bond : bond 0.00003 ( 1) link_ALPHA1-2 : bond 0.02378 ( 1) link_ALPHA1-2 : angle 2.71268 ( 3) link_ALPHA1-3 : bond 0.00351 ( 4) link_ALPHA1-3 : angle 3.12630 ( 12) link_ALPHA1-4 : bond 0.01589 ( 2) link_ALPHA1-4 : angle 4.08701 ( 6) link_ALPHA1-6 : bond 0.01434 ( 4) link_ALPHA1-6 : angle 2.52023 ( 12) link_BETA1-4 : bond 0.00265 ( 5) link_BETA1-4 : angle 2.83112 ( 15) link_BETA1-6 : bond 0.01290 ( 1) link_BETA1-6 : angle 4.07193 ( 3) link_NAG-ASN : bond 0.00408 ( 3) link_NAG-ASN : angle 2.52012 ( 9) *********************** 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 139 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.9221 (tttp) cc_final: 0.8984 (ttpt) REVERT: D 73 ASP cc_start: 0.9076 (t0) cc_final: 0.8539 (t0) REVERT: A 140 LYS cc_start: 0.8980 (mttm) cc_final: 0.8632 (mttp) REVERT: B 547 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8296 (tt) REVERT: E 65 LYS cc_start: 0.9245 (tttp) cc_final: 0.9034 (ttpt) REVERT: E 89 GLU cc_start: 0.9104 (pm20) cc_final: 0.8859 (pm20) REVERT: E 120 THR cc_start: 0.9273 (m) cc_final: 0.9046 (p) REVERT: F 6 GLU cc_start: 0.8897 (mp0) cc_final: 0.8636 (mp0) outliers start: 19 outliers final: 14 residues processed: 131 average time/residue: 0.1305 time to fit residues: 22.9227 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 : 0.369 ------------------------------------------------------------------------------- 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 547 LEU Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 595 GLN Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 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 1 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.095365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.061508 restraints weight = 16552.534| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 3.10 r_work: 0.2475 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10148 Z= 0.209 Angle : 0.641 9.021 13819 Z= 0.310 Chirality : 0.045 0.215 1547 Planarity : 0.004 0.038 1755 Dihedral : 14.834 125.440 1773 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.74 % Favored : 94.77 % Rotamer: Outliers : 2.08 % Allowed : 10.81 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.23), residues: 1224 helix: 2.24 (0.50), residues: 138 sheet: -0.31 (0.23), residues: 402 loop : -1.06 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.024 0.001 TYR A 162 PHE 0.021 0.002 PHE A 193 TRP 0.012 0.001 TRP F 101 HIS 0.004 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00507 (10110) covalent geometry : angle 0.60492 (13725) SS BOND : bond 0.00277 ( 17) SS BOND : angle 1.36111 ( 34) hydrogen bonds : bond 0.04391 ( 264) hydrogen bonds : angle 4.82176 ( 741) Misc. bond : bond 0.00013 ( 1) link_ALPHA1-2 : bond 0.02433 ( 1) link_ALPHA1-2 : angle 3.21081 ( 3) link_ALPHA1-3 : bond 0.00308 ( 4) link_ALPHA1-3 : angle 3.04130 ( 12) link_ALPHA1-4 : bond 0.01539 ( 2) link_ALPHA1-4 : angle 4.48225 ( 6) link_ALPHA1-6 : bond 0.01370 ( 4) link_ALPHA1-6 : angle 2.76168 ( 12) link_BETA1-4 : bond 0.00187 ( 5) link_BETA1-4 : angle 2.99712 ( 15) link_BETA1-6 : bond 0.01103 ( 1) link_BETA1-6 : angle 4.26178 ( 3) link_NAG-ASN : bond 0.00321 ( 3) link_NAG-ASN : angle 2.40254 ( 9) *********************** 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: 21 poor density : 120 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8980 (tttp) cc_final: 0.8635 (ttpt) REVERT: D 73 ASP cc_start: 0.8631 (t0) cc_final: 0.7840 (t0) REVERT: A 140 LYS cc_start: 0.8609 (mttm) cc_final: 0.8216 (mttp) REVERT: B 547 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7785 (tt) REVERT: B 597 TRP cc_start: 0.6577 (m-90) cc_final: 0.6242 (m-90) REVERT: C 184 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8522 (pp) REVERT: E 65 LYS cc_start: 0.9006 (tttp) cc_final: 0.8710 (ttpt) REVERT: E 89 GLU cc_start: 0.9133 (pm20) cc_final: 0.8845 (pm20) REVERT: E 120 THR cc_start: 0.9119 (m) cc_final: 0.8839 (p) REVERT: F 6 GLU cc_start: 0.8749 (mp0) cc_final: 0.8398 (mp0) outliers start: 21 outliers final: 15 residues processed: 132 average time/residue: 0.1296 time to fit residues: 22.9792 Evaluate side-chains 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 A residue 595 GLN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 overall best weight: 1.0018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.062529 restraints weight = 16467.310| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 3.10 r_work: 0.2492 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1800 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= 0.152 Angle : 0.616 8.320 13819 Z= 0.296 Chirality : 0.044 0.224 1547 Planarity : 0.004 0.037 1755 Dihedral : 14.342 123.669 1773 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.17 % Favored : 95.42 % Rotamer: Outliers : 1.79 % Allowed : 12.10 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.23), residues: 1224 helix: 2.23 (0.50), residues: 138 sheet: -0.30 (0.24), residues: 387 loop : -1.03 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 27 TYR 0.024 0.001 TYR A 162 PHE 0.018 0.001 PHE A 193 TRP 0.014 0.001 TRP A 597 HIS 0.009 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00357 (10110) covalent geometry : angle 0.58102 (13725) SS BOND : bond 0.00211 ( 17) SS BOND : angle 1.23192 ( 34) hydrogen bonds : bond 0.04010 ( 264) hydrogen bonds : angle 4.70481 ( 741) Misc. bond : bond 0.00011 ( 1) link_ALPHA1-2 : bond 0.02416 ( 1) link_ALPHA1-2 : angle 3.10006 ( 3) link_ALPHA1-3 : bond 0.00326 ( 4) link_ALPHA1-3 : angle 3.07565 ( 12) link_ALPHA1-4 : bond 0.01622 ( 2) link_ALPHA1-4 : angle 4.19749 ( 6) link_ALPHA1-6 : bond 0.01416 ( 4) link_ALPHA1-6 : angle 2.66689 ( 12) link_BETA1-4 : bond 0.00209 ( 5) link_BETA1-4 : angle 2.90611 ( 15) link_BETA1-6 : bond 0.01138 ( 1) link_BETA1-6 : angle 4.23777 ( 3) link_NAG-ASN : bond 0.00342 ( 3) link_NAG-ASN : angle 2.30039 ( 9) *********************** 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 : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 6 GLU cc_start: 0.8725 (mp0) cc_final: 0.8451 (mp0) REVERT: D 65 LYS cc_start: 0.8969 (tttp) cc_final: 0.8632 (ttpt) REVERT: D 73 ASP cc_start: 0.8617 (t0) cc_final: 0.7970 (t0) REVERT: A 140 LYS cc_start: 0.8616 (mttm) cc_final: 0.8228 (mttp) REVERT: B 50 LYS cc_start: 0.7360 (mppt) cc_final: 0.7079 (mppt) REVERT: B 547 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 597 TRP cc_start: 0.6575 (m-90) cc_final: 0.6294 (m-90) REVERT: E 65 LYS cc_start: 0.8986 (tttp) cc_final: 0.8691 (ttpt) REVERT: E 89 GLU cc_start: 0.9138 (pm20) cc_final: 0.8839 (pm20) REVERT: F 6 GLU cc_start: 0.8693 (mp0) cc_final: 0.8312 (mp0) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 0.1327 time to fit residues: 23.0445 Evaluate side-chains 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 A residue 595 GLN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 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 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 0.0370 chunk 62 optimal weight: 0.0970 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.097626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.063647 restraints weight = 16387.492| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.11 r_work: 0.2516 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10148 Z= 0.121 Angle : 0.604 7.809 13819 Z= 0.290 Chirality : 0.044 0.223 1547 Planarity : 0.004 0.036 1755 Dihedral : 13.807 122.233 1773 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.08 % Favored : 95.51 % Rotamer: Outliers : 1.69 % Allowed : 12.20 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.23), residues: 1224 helix: 2.22 (0.50), residues: 138 sheet: -0.24 (0.24), residues: 387 loop : -0.99 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 27 TYR 0.023 0.001 TYR A 162 PHE 0.016 0.001 PHE A 193 TRP 0.017 0.001 TRP A 597 HIS 0.009 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00272 (10110) covalent geometry : angle 0.56941 (13725) SS BOND : bond 0.00374 ( 17) SS BOND : angle 1.53062 ( 34) hydrogen bonds : bond 0.03639 ( 264) hydrogen bonds : angle 4.59318 ( 741) Misc. bond : bond 0.00006 ( 1) link_ALPHA1-2 : bond 0.02426 ( 1) link_ALPHA1-2 : angle 2.97375 ( 3) link_ALPHA1-3 : bond 0.00395 ( 4) link_ALPHA1-3 : angle 3.05609 ( 12) link_ALPHA1-4 : bond 0.01591 ( 2) link_ALPHA1-4 : angle 3.98763 ( 6) link_ALPHA1-6 : bond 0.01416 ( 4) link_ALPHA1-6 : angle 2.48231 ( 12) link_BETA1-4 : bond 0.00315 ( 5) link_BETA1-4 : angle 2.78558 ( 15) link_BETA1-6 : bond 0.01144 ( 1) link_BETA1-6 : angle 4.23711 ( 3) link_NAG-ASN : bond 0.00402 ( 3) link_NAG-ASN : angle 2.13584 ( 9) *********************** 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 137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8955 (tttp) cc_final: 0.8618 (ttpt) REVERT: D 73 ASP cc_start: 0.8607 (t0) cc_final: 0.7948 (t0) REVERT: A 140 LYS cc_start: 0.8633 (mttm) cc_final: 0.8247 (mttp) REVERT: A 597 TRP cc_start: 0.6505 (m-90) cc_final: 0.6276 (m-90) REVERT: B 547 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7724 (tt) REVERT: E 65 LYS cc_start: 0.8974 (tttp) cc_final: 0.8681 (ttpt) REVERT: E 89 GLU cc_start: 0.9138 (pm20) cc_final: 0.8832 (pm20) REVERT: F 6 GLU cc_start: 0.8657 (mp0) cc_final: 0.8264 (mp0) outliers start: 17 outliers final: 13 residues processed: 131 average time/residue: 0.1255 time to fit residues: 22.1004 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 : 0.357 ------------------------------------------------------------------------------- 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 547 LEU Chi-restraints excluded: chain B residue 595 GLN Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 118 GLN 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 = 0.096553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.062607 restraints weight = 16202.981| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 3.12 r_work: 0.2516 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10148 Z= 0.131 Angle : 0.608 8.233 13819 Z= 0.291 Chirality : 0.044 0.206 1547 Planarity : 0.004 0.038 1755 Dihedral : 13.331 120.578 1773 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.33 % Favored : 95.26 % Rotamer: Outliers : 1.39 % Allowed : 12.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.23), residues: 1224 helix: 2.16 (0.50), residues: 138 sheet: -0.19 (0.24), residues: 387 loop : -0.96 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 27 TYR 0.023 0.001 TYR A 162 PHE 0.017 0.001 PHE A 193 TRP 0.038 0.001 TRP B 597 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00305 (10110) covalent geometry : angle 0.57404 (13725) SS BOND : bond 0.00222 ( 17) SS BOND : angle 1.33323 ( 34) hydrogen bonds : bond 0.03692 ( 264) hydrogen bonds : angle 4.47985 ( 741) Misc. bond : bond 0.00007 ( 1) link_ALPHA1-2 : bond 0.02359 ( 1) link_ALPHA1-2 : angle 2.97902 ( 3) link_ALPHA1-3 : bond 0.00390 ( 4) link_ALPHA1-3 : angle 2.97512 ( 12) link_ALPHA1-4 : bond 0.01604 ( 2) link_ALPHA1-4 : angle 4.10164 ( 6) link_ALPHA1-6 : bond 0.01389 ( 4) link_ALPHA1-6 : angle 2.51381 ( 12) link_BETA1-4 : bond 0.00275 ( 5) link_BETA1-4 : angle 2.80634 ( 15) link_BETA1-6 : bond 0.00853 ( 1) link_BETA1-6 : angle 4.51426 ( 3) link_NAG-ASN : bond 0.00354 ( 3) link_NAG-ASN : angle 2.09283 ( 9) *********************** 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 : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8908 (tttp) cc_final: 0.8566 (ttpt) REVERT: D 73 ASP cc_start: 0.8543 (t0) cc_final: 0.7879 (t0) REVERT: A 140 LYS cc_start: 0.8579 (mttm) cc_final: 0.8201 (mttp) REVERT: B 547 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7585 (tt) REVERT: E 65 LYS cc_start: 0.8936 (tttp) cc_final: 0.8639 (ttpt) REVERT: E 89 GLU cc_start: 0.9140 (pm20) cc_final: 0.8853 (pm20) REVERT: F 6 GLU cc_start: 0.8606 (mp0) cc_final: 0.8185 (mp0) outliers start: 14 outliers final: 13 residues processed: 134 average time/residue: 0.1358 time to fit residues: 23.7892 Evaluate side-chains 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain 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 117 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 HIS B 550 ASN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.060382 restraints weight = 16339.298| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 3.14 r_work: 0.2470 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10148 Z= 0.204 Angle : 0.659 9.010 13819 Z= 0.318 Chirality : 0.045 0.187 1547 Planarity : 0.004 0.041 1755 Dihedral : 13.284 120.733 1773 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.82 % Favored : 94.69 % Rotamer: Outliers : 1.29 % Allowed : 12.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.23), residues: 1224 helix: 2.20 (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 ARG 0.008 0.000 ARG F 27 TYR 0.023 0.001 TYR A 162 PHE 0.022 0.002 PHE A 193 TRP 0.026 0.002 TRP A 597 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00492 (10110) covalent geometry : angle 0.62079 (13725) SS BOND : bond 0.00233 ( 17) SS BOND : angle 1.60107 ( 34) hydrogen bonds : bond 0.04371 ( 264) hydrogen bonds : angle 4.59859 ( 741) Misc. bond : bond 0.00017 ( 1) link_ALPHA1-2 : bond 0.02405 ( 1) link_ALPHA1-2 : angle 2.98740 ( 3) link_ALPHA1-3 : bond 0.00317 ( 4) link_ALPHA1-3 : angle 2.92649 ( 12) link_ALPHA1-4 : bond 0.01592 ( 2) link_ALPHA1-4 : angle 4.67477 ( 6) link_ALPHA1-6 : bond 0.01329 ( 4) link_ALPHA1-6 : angle 2.91293 ( 12) link_BETA1-4 : bond 0.00186 ( 5) link_BETA1-4 : angle 3.03216 ( 15) link_BETA1-6 : bond 0.00230 ( 1) link_BETA1-6 : angle 5.04013 ( 3) link_NAG-ASN : bond 0.00263 ( 3) link_NAG-ASN : angle 2.26877 ( 9) *********************** 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 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8936 (tttp) cc_final: 0.8590 (ttpt) REVERT: D 73 ASP cc_start: 0.8598 (t0) cc_final: 0.7943 (t0) REVERT: B 547 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7738 (tt) REVERT: E 65 LYS cc_start: 0.8961 (tttp) cc_final: 0.8657 (ttpt) REVERT: E 89 GLU cc_start: 0.9169 (pm20) cc_final: 0.8889 (pm20) REVERT: F 6 GLU cc_start: 0.8584 (mp0) cc_final: 0.8208 (mp0) outliers start: 13 outliers final: 12 residues processed: 129 average time/residue: 0.1326 time to fit residues: 22.6246 Evaluate side-chains 130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain 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 38 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.096392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.062385 restraints weight = 16278.667| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 3.11 r_work: 0.2497 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2003 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= 0.160 Angle : 0.628 8.115 13819 Z= 0.302 Chirality : 0.044 0.178 1547 Planarity : 0.004 0.042 1755 Dihedral : 12.917 123.958 1773 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.41 % Favored : 95.26 % Rotamer: Outliers : 1.29 % Allowed : 12.90 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.23), residues: 1224 helix: 2.19 (0.50), residues: 138 sheet: -0.21 (0.24), residues: 387 loop : -1.02 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 27 TYR 0.023 0.001 TYR A 162 PHE 0.017 0.001 PHE A 193 TRP 0.030 0.001 TRP A 597 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00381 (10110) covalent geometry : angle 0.59146 (13725) SS BOND : bond 0.00232 ( 17) SS BOND : angle 1.30033 ( 34) hydrogen bonds : bond 0.03920 ( 264) hydrogen bonds : angle 4.52995 ( 741) Misc. bond : bond 0.00015 ( 1) link_ALPHA1-2 : bond 0.02331 ( 1) link_ALPHA1-2 : angle 2.70819 ( 3) link_ALPHA1-3 : bond 0.00382 ( 4) link_ALPHA1-3 : angle 3.03172 ( 12) link_ALPHA1-4 : bond 0.01527 ( 2) link_ALPHA1-4 : angle 4.39483 ( 6) link_ALPHA1-6 : bond 0.01346 ( 4) link_ALPHA1-6 : angle 2.87554 ( 12) link_BETA1-4 : bond 0.00208 ( 5) link_BETA1-4 : angle 2.98400 ( 15) link_BETA1-6 : bond 0.00292 ( 1) link_BETA1-6 : angle 4.56389 ( 3) link_NAG-ASN : bond 0.00333 ( 3) link_NAG-ASN : angle 2.18061 ( 9) ********************** 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 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LYS cc_start: 0.8967 (tttp) cc_final: 0.8630 (ttpt) REVERT: D 73 ASP cc_start: 0.8659 (t0) cc_final: 0.7999 (t0) REVERT: B 547 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7792 (tt) REVERT: E 65 LYS cc_start: 0.8993 (tttp) cc_final: 0.8699 (ttpt) REVERT: E 89 GLU cc_start: 0.9171 (pm20) cc_final: 0.8894 (pm20) REVERT: F 6 GLU cc_start: 0.8631 (mp0) cc_final: 0.8217 (mp0) outliers start: 13 outliers final: 12 residues processed: 128 average time/residue: 0.1255 time to fit residues: 21.4412 Evaluate side-chains 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain 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 98 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.095975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.061922 restraints weight = 16320.122| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.15 r_work: 0.2500 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10148 Z= 0.128 Angle : 0.611 7.586 13819 Z= 0.295 Chirality : 0.044 0.179 1547 Planarity : 0.004 0.050 1755 Dihedral : 12.731 125.394 1773 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.25 % Favored : 95.42 % Rotamer: Outliers : 1.29 % Allowed : 13.10 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.23), residues: 1224 helix: 2.17 (0.50), residues: 138 sheet: -0.18 (0.24), residues: 387 loop : -0.99 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 27 TYR 0.023 0.001 TYR A 162 PHE 0.016 0.001 PHE A 193 TRP 0.030 0.001 TRP A 597 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00297 (10110) covalent geometry : angle 0.57673 (13725) SS BOND : bond 0.00205 ( 17) SS BOND : angle 1.21987 ( 34) hydrogen bonds : bond 0.03743 ( 264) hydrogen bonds : angle 4.49522 ( 741) Misc. bond : bond 0.00010 ( 1) link_ALPHA1-2 : bond 0.02352 ( 1) link_ALPHA1-2 : angle 2.62463 ( 3) link_ALPHA1-3 : bond 0.00437 ( 4) link_ALPHA1-3 : angle 3.03876 ( 12) link_ALPHA1-4 : bond 0.01487 ( 2) link_ALPHA1-4 : angle 4.23288 ( 6) link_ALPHA1-6 : bond 0.01348 ( 4) link_ALPHA1-6 : angle 2.76641 ( 12) link_BETA1-4 : bond 0.00273 ( 5) link_BETA1-4 : angle 2.86952 ( 15) link_BETA1-6 : bond 0.00293 ( 1) link_BETA1-6 : angle 4.20248 ( 3) link_NAG-ASN : bond 0.00356 ( 3) link_NAG-ASN : angle 2.11298 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2306.52 seconds wall clock time: 40 minutes 20.34 seconds (2420.34 seconds total)