Starting phenix.real_space_refine on Sat Sep 12 02:50:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u5p_20652/09_2026/6u5p_20652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5p_20652/09_2026/6u5p_20652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u5p_20652/09_2026/6u5p_20652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5p_20652/09_2026/6u5p_20652.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6u5p_20652/09_2026/6u5p_20652.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u5p_20652/09_2026/6u5p_20652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u5p_20652/09_2026/6u5p_20652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5p_20652/09_2026/6u5p_20652.map" } resolution = 3.3 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= 0.005 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: 5 Type Number sf(0) Gaussians Ca 24 9.91 5 S 56 5.16 5 C 8322 2.51 5 N 2378 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13308 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1650 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1678 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1658 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "F" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1650 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1678 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1658 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "H" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.36, per 1000 atoms: 0.18 Number of scatterers: 13308 At special positions: 0 Unit cell: (139.192, 139.192, 64.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 24 19.99 S 56 16.00 O 2528 8.00 N 2378 7.00 C 8322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 433.9 milliseconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 16 sheets defined 45.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.807A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.535A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.502A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.831A pdb=" N VAL A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 148 through 155 removed outlier: 3.813A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.704A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.649A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.585A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.592A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.548A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 3.563A pdb=" N ASP E 284 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.791A pdb=" N ALA B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.693A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.531A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.940A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.709A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.582A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 241 removed outlier: 3.565A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.790A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.600A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.583A pdb=" N VAL F 288 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 148 through 156 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.807A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.535A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.503A pdb=" N MET C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.831A pdb=" N VAL C 288 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.812A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.705A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.648A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.588A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.590A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.548A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.562A pdb=" N ASP G 284 " --> pdb=" O VAL G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 334 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 148 through 156 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.790A pdb=" N ALA D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.694A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.532A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 148 through 154 Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.941A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.709A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.583A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 241 removed outlier: 3.564A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 256 removed outlier: 3.788A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.598A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.583A pdb=" N VAL H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.408A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 7.389A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.500A pdb=" N VAL E 139 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL E 160 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 141 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA E 209 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 7.219A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.549A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS B 117 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 180 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE B 208 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 207 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 209 " --> pdb=" O ILE B 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 268 removed outlier: 7.240A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.391A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 7.230A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.408A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.719A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.499A pdb=" N VAL G 139 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL G 160 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL G 141 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA G 209 " --> pdb=" O ILE G 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 7.220A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.549A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS D 117 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA D 180 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE D 208 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE D 229 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA D 209 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 7.239A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.391A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 7.230A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1707 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: 1.63 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4011 1.33 - 1.45: 1578 1.45 - 1.57: 7767 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 13444 Sorted by residual: bond pdb=" CG GLN B 227 " pdb=" CD GLN B 227 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.80e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CG GLN D 227 " pdb=" CD GLN D 227 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.68e+00 bond pdb=" CG1 ILE A 195 " pdb=" CD1 ILE A 195 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG LEU D 220 " pdb=" CD2 LEU D 220 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.66e+00 ... (remaining 13439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 16596 1.23 - 2.45: 1354 2.45 - 3.68: 198 3.68 - 4.91: 56 4.91 - 6.13: 4 Bond angle restraints: 18208 Sorted by residual: angle pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 111.28 114.64 -3.36 1.09e+00 8.42e-01 9.51e+00 angle pdb=" N GLU D 171 " pdb=" CA GLU D 171 " pdb=" C GLU D 171 " ideal model delta sigma weight residual 111.28 114.63 -3.35 1.09e+00 8.42e-01 9.43e+00 angle pdb=" N GLY D 162 " pdb=" CA GLY D 162 " pdb=" C GLY D 162 " ideal model delta sigma weight residual 110.88 115.28 -4.40 1.48e+00 4.57e-01 8.82e+00 angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 110.88 115.26 -4.38 1.48e+00 4.57e-01 8.76e+00 angle pdb=" C LEU B 170 " pdb=" N GLU B 171 " pdb=" CA GLU B 171 " ideal model delta sigma weight residual 120.28 124.05 -3.77 1.34e+00 5.57e-01 7.93e+00 ... (remaining 18203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 7248 16.60 - 33.21: 783 33.21 - 49.81: 131 49.81 - 66.41: 28 66.41 - 83.02: 18 Dihedral angle restraints: 8208 sinusoidal: 3144 harmonic: 5064 Sorted by residual: dihedral pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " pdb=" CG ASP A 287 " pdb=" OD1 ASP A 287 " ideal model delta sinusoidal sigma weight residual -30.00 -82.92 52.92 1 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CA ASP C 287 " pdb=" CB ASP C 287 " pdb=" CG ASP C 287 " pdb=" OD1 ASP C 287 " ideal model delta sinusoidal sigma weight residual -30.00 -82.89 52.89 1 2.00e+01 2.50e-03 9.52e+00 dihedral pdb=" N LYS G 200 " pdb=" CA LYS G 200 " pdb=" CB LYS G 200 " pdb=" CG LYS G 200 " ideal model delta sinusoidal sigma weight residual -60.00 -116.90 56.90 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1467 0.046 - 0.092: 465 0.092 - 0.137: 218 0.137 - 0.183: 22 0.183 - 0.229: 4 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CB ILE B 303 " pdb=" CA ILE B 303 " pdb=" CG1 ILE B 303 " pdb=" CG2 ILE B 303 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE D 303 " pdb=" CA ILE D 303 " pdb=" CG1 ILE D 303 " pdb=" CG2 ILE D 303 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL B 205 " pdb=" CA VAL B 205 " pdb=" CG1 VAL B 205 " pdb=" CG2 VAL B 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2173 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 169 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C ASP D 169 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP D 169 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 169 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ASP B 169 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP B 169 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU B 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 267 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C VAL B 267 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL B 267 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO B 268 " 0.012 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2404 2.77 - 3.30: 11435 3.30 - 3.83: 21451 3.83 - 4.37: 24497 4.37 - 4.90: 45416 Nonbonded interactions: 105203 Sorted by model distance: nonbonded pdb=" OG SER C 124 " pdb=" OD2 ASP C 184 " model vdw 2.236 3.040 nonbonded pdb=" OG SER A 124 " pdb=" OD2 ASP A 184 " model vdw 2.236 3.040 nonbonded pdb=" O ILE A 285 " pdb=" OG1 THR A 289 " model vdw 2.278 3.040 nonbonded pdb=" O ILE C 285 " pdb=" OG1 THR C 289 " model vdw 2.280 3.040 nonbonded pdb=" OG SER E 124 " pdb=" OD2 ASP E 184 " model vdw 2.282 3.040 ... (remaining 105198 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 0.850 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.010 Find NCS groups from input model: 0.070 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 0.051 13444 Z= 0.249 Angle : 0.750 6.134 18208 Z= 0.456 Chirality : 0.053 0.229 2176 Planarity : 0.005 0.048 2372 Dihedral : 14.368 83.017 4944 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.43 % Allowed : 7.33 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.15), residues: 1760 helix: -3.01 (0.12), residues: 832 sheet: 0.58 (0.24), residues: 352 loop : -2.58 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 298 TYR 0.011 0.002 TYR G 247 PHE 0.009 0.001 PHE E 251 TRP 0.003 0.001 TRP B 123 HIS 0.014 0.002 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (13444) covalent geometry : angle 0.74996 / 0.46 (18208) hydrogen bonds : bond 0.18294 / 12.68 ( 597) hydrogen bonds : angle 6.91270 / 4.92 ( 1707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 328 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7460 (mtt180) cc_final: 0.7198 (mtm-85) REVERT: A 247 TYR cc_start: 0.8720 (m-80) cc_final: 0.7775 (m-80) REVERT: A 333 TYR cc_start: 0.7628 (t80) cc_final: 0.7259 (t80) REVERT: E 154 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7545 (mtm-85) REVERT: E 190 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7096 (mt-10) REVERT: E 266 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8442 (mt-10) REVERT: E 303 ILE cc_start: 0.8591 (mt) cc_final: 0.8080 (mm) REVERT: E 310 TYR cc_start: 0.7930 (t80) cc_final: 0.7450 (t80) REVERT: B 239 MET cc_start: 0.8673 (mtm) cc_final: 0.8368 (mtm) REVERT: F 266 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7959 (mt-10) REVERT: F 303 ILE cc_start: 0.8476 (mt) cc_final: 0.8204 (mm) REVERT: C 132 ARG cc_start: 0.7462 (mtt180) cc_final: 0.7193 (mtm-85) REVERT: C 247 TYR cc_start: 0.8718 (m-80) cc_final: 0.7774 (m-80) REVERT: C 333 TYR cc_start: 0.7602 (t80) cc_final: 0.7251 (t80) REVERT: G 154 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7504 (mtm-85) REVERT: G 190 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7107 (mt-10) REVERT: G 266 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8445 (mt-10) REVERT: G 303 ILE cc_start: 0.8600 (mt) cc_final: 0.8097 (mm) REVERT: G 310 TYR cc_start: 0.7898 (t80) cc_final: 0.7410 (t80) REVERT: D 239 MET cc_start: 0.8673 (mtm) cc_final: 0.8365 (mtm) REVERT: H 266 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7971 (mt-10) REVERT: H 303 ILE cc_start: 0.8481 (mt) cc_final: 0.8211 (mm) outliers start: 6 outliers final: 6 residues processed: 330 average time/residue: 0.1490 time to fit residues: 65.1435 Evaluate side-chains 243 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 237 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain H residue 245 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.152272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113808 restraints weight = 14455.838| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.97 r_work: 0.2965 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13444 Z= 0.178 Angle : 0.500 4.701 18208 Z= 0.269 Chirality : 0.049 0.166 2176 Planarity : 0.004 0.031 2372 Dihedral : 4.389 30.360 1954 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.15 % Allowed : 13.72 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 1760 helix: -1.19 (0.17), residues: 784 sheet: 0.45 (0.26), residues: 304 loop : -2.07 (0.18), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 149 TYR 0.008 0.001 TYR B 247 PHE 0.004 0.001 PHE G 251 TRP 0.003 0.001 TRP D 123 HIS 0.009 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (13444) covalent geometry : angle 0.50034 / 0.27 (18208) hydrogen bonds : bond 0.04376 / 3.06 ( 597) hydrogen bonds : angle 4.80413 / 3.39 ( 1707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7583 (mtt180) cc_final: 0.6953 (mtm-85) REVERT: A 222 MET cc_start: 0.7065 (ptt) cc_final: 0.6770 (mtp) REVERT: A 333 TYR cc_start: 0.7490 (t80) cc_final: 0.6830 (t80) REVERT: E 154 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.7987 (mtm-85) REVERT: E 190 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7898 (mt-10) REVERT: E 303 ILE cc_start: 0.8117 (mt) cc_final: 0.7621 (mm) REVERT: E 310 TYR cc_start: 0.7499 (t80) cc_final: 0.6772 (t80) REVERT: B 132 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7695 (ttm170) REVERT: B 212 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7602 (mp0) REVERT: B 213 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8320 (ttm170) REVERT: B 239 MET cc_start: 0.8906 (mtm) cc_final: 0.8627 (mtm) REVERT: C 132 ARG cc_start: 0.7571 (mtt180) cc_final: 0.6938 (mtm-85) REVERT: C 333 TYR cc_start: 0.7478 (t80) cc_final: 0.6823 (t80) REVERT: G 154 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.8056 (mtm-85) REVERT: G 190 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7899 (mt-10) REVERT: G 303 ILE cc_start: 0.8199 (mt) cc_final: 0.7695 (mm) REVERT: G 310 TYR cc_start: 0.7493 (t80) cc_final: 0.6760 (t80) REVERT: D 132 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7677 (ttm170) REVERT: D 212 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7604 (mp0) REVERT: D 213 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8328 (ttm170) REVERT: D 239 MET cc_start: 0.8911 (mtm) cc_final: 0.8629 (mtm) outliers start: 16 outliers final: 14 residues processed: 258 average time/residue: 0.1358 time to fit residues: 47.6745 Evaluate side-chains 255 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 115 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 164 optimal weight: 0.2980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.153412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.114780 restraints weight = 14433.272| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.02 r_work: 0.2942 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13444 Z= 0.114 Angle : 0.434 5.177 18208 Z= 0.232 Chirality : 0.047 0.151 2176 Planarity : 0.003 0.026 2372 Dihedral : 3.581 12.176 1942 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.58 % Allowed : 15.73 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.18), residues: 1760 helix: -0.34 (0.19), residues: 784 sheet: 0.32 (0.26), residues: 304 loop : -1.65 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.007 0.001 TYR C 333 PHE 0.004 0.001 PHE A 312 TRP 0.002 0.001 TRP A 123 HIS 0.005 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 (13444) covalent geometry : angle 0.43351 / 0.23 (18208) hydrogen bonds : bond 0.03469 / 2.43 ( 597) hydrogen bonds : angle 4.36266 / 3.07 ( 1707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7125 (mtm-85) REVERT: A 222 MET cc_start: 0.6978 (ptt) cc_final: 0.6739 (mtp) REVERT: A 333 TYR cc_start: 0.7497 (t80) cc_final: 0.6994 (t80) REVERT: E 154 ARG cc_start: 0.8471 (ttp-110) cc_final: 0.8129 (mtm-85) REVERT: E 303 ILE cc_start: 0.8147 (mt) cc_final: 0.7644 (mm) REVERT: B 212 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7740 (mp0) REVERT: B 213 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8340 (ttm170) REVERT: B 239 MET cc_start: 0.8995 (mtm) cc_final: 0.8766 (mtm) REVERT: B 305 ASP cc_start: 0.8176 (t70) cc_final: 0.7967 (t70) REVERT: F 301 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: C 132 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7109 (mtm-85) REVERT: C 333 TYR cc_start: 0.7492 (t80) cc_final: 0.6993 (t80) REVERT: G 154 ARG cc_start: 0.8466 (ttp-110) cc_final: 0.8130 (mtm-85) REVERT: G 190 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7908 (mt-10) REVERT: G 303 ILE cc_start: 0.8099 (mt) cc_final: 0.7621 (mm) REVERT: D 212 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7744 (mp0) REVERT: D 213 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8316 (ttm170) REVERT: D 239 MET cc_start: 0.9000 (mtm) cc_final: 0.8769 (mtm) REVERT: H 301 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6536 (pm20) outliers start: 22 outliers final: 12 residues processed: 262 average time/residue: 0.1429 time to fit residues: 50.0526 Evaluate side-chains 243 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 301 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 301 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.111096 restraints weight = 14713.191| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.15 r_work: 0.2887 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13444 Z= 0.236 Angle : 0.516 4.878 18208 Z= 0.272 Chirality : 0.050 0.160 2176 Planarity : 0.004 0.035 2372 Dihedral : 3.839 15.368 1942 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.37 % Allowed : 18.10 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 1760 helix: -0.23 (0.19), residues: 784 sheet: 0.10 (0.26), residues: 304 loop : -1.59 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.007 0.001 TYR E 247 PHE 0.006 0.001 PHE G 251 TRP 0.003 0.001 TRP H 123 HIS 0.011 0.002 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.24 (13444) covalent geometry : angle 0.51630 / 0.27 (18208) hydrogen bonds : bond 0.04333 / 3.04 ( 597) hydrogen bonds : angle 4.45536 / 3.14 ( 1707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7216 (mtm-85) REVERT: A 222 MET cc_start: 0.7118 (ptt) cc_final: 0.6892 (mtp) REVERT: A 333 TYR cc_start: 0.7573 (t80) cc_final: 0.7026 (t80) REVERT: E 154 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.8069 (mtm-85) REVERT: E 303 ILE cc_start: 0.8271 (mt) cc_final: 0.7718 (mm) REVERT: E 310 TYR cc_start: 0.7481 (t80) cc_final: 0.6721 (t80) REVERT: B 171 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: B 213 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8421 (ttm170) REVERT: B 239 MET cc_start: 0.8982 (mtm) cc_final: 0.8708 (mtm) REVERT: B 305 ASP cc_start: 0.8303 (t70) cc_final: 0.8037 (t70) REVERT: C 132 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7201 (mtm-85) REVERT: C 333 TYR cc_start: 0.7597 (t80) cc_final: 0.7038 (t80) REVERT: G 154 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.8076 (mtm-85) REVERT: G 303 ILE cc_start: 0.8219 (mt) cc_final: 0.7669 (mm) REVERT: G 310 TYR cc_start: 0.7436 (t80) cc_final: 0.6680 (t80) REVERT: D 171 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: D 213 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8429 (ttm170) REVERT: D 239 MET cc_start: 0.8985 (mtm) cc_final: 0.8706 (mtm) REVERT: D 305 ASP cc_start: 0.8307 (t70) cc_final: 0.8042 (t70) outliers start: 33 outliers final: 28 residues processed: 252 average time/residue: 0.1294 time to fit residues: 44.6135 Evaluate side-chains 250 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 95 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.152080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.114260 restraints weight = 14534.142| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.85 r_work: 0.2971 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13444 Z= 0.115 Angle : 0.435 8.753 18208 Z= 0.228 Chirality : 0.047 0.145 2176 Planarity : 0.003 0.028 2372 Dihedral : 3.525 13.403 1942 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.66 % Allowed : 18.89 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1760 helix: 0.11 (0.19), residues: 784 sheet: 0.11 (0.26), residues: 304 loop : -1.36 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.008 0.001 TYR A 333 PHE 0.004 0.001 PHE A 232 TRP 0.002 0.001 TRP B 123 HIS 0.005 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (13444) covalent geometry : angle 0.43531 / 0.23 (18208) hydrogen bonds : bond 0.03232 / 2.28 ( 597) hydrogen bonds : angle 4.28205 / 3.03 ( 1707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7130 (mtm-85) REVERT: A 333 TYR cc_start: 0.7488 (t80) cc_final: 0.7015 (t80) REVERT: E 154 ARG cc_start: 0.8435 (ttp-110) cc_final: 0.8132 (mtm-85) REVERT: E 266 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: E 303 ILE cc_start: 0.8158 (mt) cc_final: 0.7651 (mm) REVERT: B 171 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: B 213 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8292 (ttm170) REVERT: B 239 MET cc_start: 0.8954 (mtm) cc_final: 0.8728 (mtm) REVERT: F 188 ASP cc_start: 0.8034 (t0) cc_final: 0.7811 (t0) REVERT: C 132 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7118 (mtm-85) REVERT: C 333 TYR cc_start: 0.7481 (t80) cc_final: 0.7008 (t80) REVERT: G 154 ARG cc_start: 0.8436 (ttp-110) cc_final: 0.8137 (mtm-85) REVERT: G 190 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7749 (mt-10) REVERT: G 266 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8326 (mt-10) REVERT: G 303 ILE cc_start: 0.8132 (mt) cc_final: 0.7654 (mm) REVERT: D 213 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8288 (ttm170) REVERT: D 239 MET cc_start: 0.8959 (mtm) cc_final: 0.8732 (mtm) REVERT: H 188 ASP cc_start: 0.8031 (t0) cc_final: 0.7805 (t0) outliers start: 37 outliers final: 27 residues processed: 254 average time/residue: 0.1514 time to fit residues: 52.2619 Evaluate side-chains 245 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 6 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.114742 restraints weight = 14413.066| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.08 r_work: 0.2932 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13444 Z= 0.108 Angle : 0.431 11.621 18208 Z= 0.224 Chirality : 0.046 0.148 2176 Planarity : 0.003 0.041 2372 Dihedral : 3.373 13.660 1942 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.37 % Allowed : 19.54 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 1760 helix: 0.34 (0.19), residues: 784 sheet: 0.17 (0.26), residues: 304 loop : -1.19 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 132 TYR 0.010 0.001 TYR G 310 PHE 0.004 0.001 PHE C 312 TRP 0.002 0.000 TRP G 123 HIS 0.004 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (13444) covalent geometry : angle 0.43140 / 0.22 (18208) hydrogen bonds : bond 0.03121 / 2.19 ( 597) hydrogen bonds : angle 4.18047 / 2.95 ( 1707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7169 (mtm-85) REVERT: A 333 TYR cc_start: 0.7513 (t80) cc_final: 0.7117 (t80) REVERT: E 154 ARG cc_start: 0.8439 (ttp-110) cc_final: 0.8106 (mtm-85) REVERT: E 190 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7869 (mt-10) REVERT: E 266 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: E 303 ILE cc_start: 0.8217 (mt) cc_final: 0.7659 (mm) REVERT: B 132 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7893 (ttm170) REVERT: B 171 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8201 (mt-10) REVERT: B 213 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8335 (ttm170) REVERT: B 239 MET cc_start: 0.8984 (mtm) cc_final: 0.8777 (mtm) REVERT: C 132 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7166 (mtm-85) REVERT: C 333 TYR cc_start: 0.7515 (t80) cc_final: 0.7101 (t80) REVERT: G 154 ARG cc_start: 0.8441 (ttp-110) cc_final: 0.8118 (mtm-85) REVERT: G 190 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7858 (mt-10) REVERT: G 266 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8359 (mt-10) REVERT: G 303 ILE cc_start: 0.8161 (mt) cc_final: 0.7616 (mm) REVERT: D 132 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7889 (ttm170) REVERT: D 213 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.8331 (ttm170) REVERT: D 239 MET cc_start: 0.8981 (mtm) cc_final: 0.8772 (mtm) REVERT: D 305 ASP cc_start: 0.8129 (t70) cc_final: 0.7878 (t70) REVERT: H 153 LEU cc_start: 0.6915 (mp) cc_final: 0.6621 (mp) outliers start: 33 outliers final: 25 residues processed: 247 average time/residue: 0.1480 time to fit residues: 49.8565 Evaluate side-chains 249 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 50 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113888 restraints weight = 14359.512| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.03 r_work: 0.2935 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13444 Z= 0.110 Angle : 0.437 11.145 18208 Z= 0.225 Chirality : 0.046 0.148 2176 Planarity : 0.003 0.040 2372 Dihedral : 3.323 13.770 1942 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.37 % Allowed : 20.11 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 1760 helix: 0.45 (0.19), residues: 784 sheet: 0.20 (0.26), residues: 304 loop : -1.09 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 132 TYR 0.009 0.001 TYR G 310 PHE 0.007 0.001 PHE G 251 TRP 0.002 0.000 TRP E 123 HIS 0.004 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (13444) covalent geometry : angle 0.43692 / 0.22 (18208) hydrogen bonds : bond 0.03120 / 2.19 ( 597) hydrogen bonds : angle 4.14289 / 2.93 ( 1707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7592 (mtt180) cc_final: 0.7175 (mtm-85) REVERT: A 333 TYR cc_start: 0.7500 (t80) cc_final: 0.7061 (t80) REVERT: E 154 ARG cc_start: 0.8448 (ttp-110) cc_final: 0.8100 (mtm-85) REVERT: E 190 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7872 (mt-10) REVERT: E 266 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: E 303 ILE cc_start: 0.8204 (mt) cc_final: 0.7648 (mm) REVERT: B 132 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7754 (ttm170) REVERT: B 171 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: B 213 ARG cc_start: 0.8602 (ttm-80) cc_final: 0.8344 (ttm170) REVERT: B 305 ASP cc_start: 0.8056 (t70) cc_final: 0.7803 (t70) REVERT: C 132 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7179 (mtm-85) REVERT: C 333 TYR cc_start: 0.7553 (t80) cc_final: 0.7123 (t80) REVERT: G 154 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.8106 (mtm-85) REVERT: G 190 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7868 (mt-10) REVERT: G 266 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: G 303 ILE cc_start: 0.8114 (mt) cc_final: 0.7572 (mm) REVERT: D 132 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7767 (ttm170) REVERT: D 213 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8337 (ttm170) outliers start: 33 outliers final: 26 residues processed: 243 average time/residue: 0.1504 time to fit residues: 49.6597 Evaluate side-chains 244 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 119 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.0040 chunk 91 optimal weight: 2.9990 chunk 164 optimal weight: 0.0870 overall best weight: 0.9974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.152276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.114152 restraints weight = 14306.638| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.99 r_work: 0.2934 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13444 Z= 0.122 Angle : 0.428 5.365 18208 Z= 0.225 Chirality : 0.047 0.152 2176 Planarity : 0.003 0.039 2372 Dihedral : 3.339 14.185 1942 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.59 % Allowed : 19.68 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 1760 helix: 0.48 (0.19), residues: 784 sheet: 0.21 (0.26), residues: 304 loop : -1.04 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 132 TYR 0.009 0.001 TYR G 310 PHE 0.006 0.001 PHE G 251 TRP 0.002 0.001 TRP B 123 HIS 0.005 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 (13444) covalent geometry : angle 0.42800 / 0.22 (18208) hydrogen bonds : bond 0.03200 / 2.25 ( 597) hydrogen bonds : angle 4.11915 / 2.92 ( 1707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7364 (mtm-85) REVERT: A 333 TYR cc_start: 0.7529 (t80) cc_final: 0.7005 (t80) REVERT: E 154 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.8159 (mtm-85) REVERT: E 190 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7918 (mt-10) REVERT: E 266 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: E 303 ILE cc_start: 0.8260 (mt) cc_final: 0.7690 (mm) REVERT: B 132 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: B 171 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: B 213 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8384 (ttm170) REVERT: C 132 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7361 (mtm-85) REVERT: C 333 TYR cc_start: 0.7580 (t80) cc_final: 0.7057 (t80) REVERT: G 154 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.8162 (mtm-85) REVERT: G 190 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7908 (mt-10) REVERT: G 266 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: G 303 ILE cc_start: 0.8196 (mt) cc_final: 0.7638 (mm) REVERT: D 132 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: D 213 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8376 (ttm170) REVERT: D 305 ASP cc_start: 0.8069 (t70) cc_final: 0.7824 (t70) outliers start: 36 outliers final: 30 residues processed: 248 average time/residue: 0.1442 time to fit residues: 49.0248 Evaluate side-chains 234 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 82 optimal weight: 0.0370 chunk 149 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 151 optimal weight: 0.0170 chunk 175 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.154196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.115986 restraints weight = 14393.204| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.01 r_work: 0.2962 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13444 Z= 0.081 Angle : 0.424 10.814 18208 Z= 0.218 Chirality : 0.046 0.149 2176 Planarity : 0.003 0.037 2372 Dihedral : 3.171 14.154 1942 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.44 % Allowed : 20.55 % Favored : 77.01 % 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 are not related in a simple way. whole: -0.01 (0.20), residues: 1760 helix: 0.71 (0.20), residues: 784 sheet: 0.28 (0.27), residues: 304 loop : -0.91 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.008 0.001 TYR C 333 PHE 0.005 0.000 PHE E 251 TRP 0.003 0.000 TRP G 123 HIS 0.002 0.000 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.08 (13444) covalent geometry : angle 0.42412 / 0.22 (18208) hydrogen bonds : bond 0.02754 / 1.93 ( 597) hydrogen bonds : angle 4.07454 / 2.88 ( 1707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7303 (mtm-85) REVERT: A 333 TYR cc_start: 0.7488 (t80) cc_final: 0.7037 (t80) REVERT: E 154 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.8208 (mtm-85) REVERT: E 190 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7837 (mt-10) REVERT: E 266 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: E 303 ILE cc_start: 0.8132 (mt) cc_final: 0.7577 (mm) REVERT: B 171 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: B 213 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8337 (ttm170) REVERT: B 241 ARG cc_start: 0.8366 (mtt90) cc_final: 0.8127 (mtt-85) REVERT: F 132 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7636 (ttp80) REVERT: F 285 ILE cc_start: 0.7815 (mm) cc_final: 0.7474 (mm) REVERT: C 132 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7302 (mtm-85) REVERT: C 333 TYR cc_start: 0.7496 (t80) cc_final: 0.7038 (t80) REVERT: G 154 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.8224 (mtm-85) REVERT: G 190 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7835 (mt-10) REVERT: G 266 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: G 303 ILE cc_start: 0.8160 (mt) cc_final: 0.7613 (mm) REVERT: D 213 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8290 (ttm170) REVERT: D 241 ARG cc_start: 0.8349 (mtt90) cc_final: 0.8093 (mtt-85) REVERT: H 132 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7642 (ttp80) outliers start: 34 outliers final: 26 residues processed: 254 average time/residue: 0.1439 time to fit residues: 49.5975 Evaluate side-chains 261 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 134 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.153810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.115877 restraints weight = 14402.604| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.06 r_work: 0.2953 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 13444 Z= 0.098 Angle : 0.430 9.692 18208 Z= 0.222 Chirality : 0.047 0.176 2176 Planarity : 0.003 0.039 2372 Dihedral : 3.184 14.353 1942 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.30 % Allowed : 20.62 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1760 helix: 0.72 (0.20), residues: 784 sheet: 0.28 (0.27), residues: 304 loop : -0.81 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.008 0.001 TYR G 310 PHE 0.006 0.001 PHE E 251 TRP 0.002 0.000 TRP G 123 HIS 0.003 0.000 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (13444) covalent geometry : angle 0.43028 / 0.22 (18208) hydrogen bonds : bond 0.02937 / 2.05 ( 597) hydrogen bonds : angle 4.06236 / 2.87 ( 1707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7244 (mtm-85) REVERT: A 333 TYR cc_start: 0.7496 (t80) cc_final: 0.7051 (t80) REVERT: E 154 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.8150 (mtm-85) REVERT: E 190 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7852 (mt-10) REVERT: E 266 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: E 303 ILE cc_start: 0.8142 (mt) cc_final: 0.7593 (mm) REVERT: B 171 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: B 213 ARG cc_start: 0.8612 (ttm-80) cc_final: 0.8360 (ttm170) REVERT: B 241 ARG cc_start: 0.8379 (mtt90) cc_final: 0.8147 (mtt-85) REVERT: C 132 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7260 (mtm-85) REVERT: C 313 ARG cc_start: 0.4840 (mtm-85) cc_final: 0.4587 (mtm-85) REVERT: C 333 TYR cc_start: 0.7486 (t80) cc_final: 0.7058 (t80) REVERT: G 154 ARG cc_start: 0.8516 (ttp-110) cc_final: 0.8238 (mtm-85) REVERT: G 190 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7881 (mt-10) REVERT: G 266 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: G 303 ILE cc_start: 0.8163 (mt) cc_final: 0.7615 (mm) REVERT: D 213 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8310 (ttm170) REVERT: D 241 ARG cc_start: 0.8373 (mtt90) cc_final: 0.8123 (mtt-85) REVERT: H 132 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7614 (ttp80) outliers start: 32 outliers final: 27 residues processed: 243 average time/residue: 0.1455 time to fit residues: 48.8585 Evaluate side-chains 253 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain F residue 151 LYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 222 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 16 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 36 optimal weight: 0.0170 chunk 160 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.153753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.115730 restraints weight = 14413.829| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.90 r_work: 0.2993 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13444 Z= 0.101 Angle : 0.426 9.304 18208 Z= 0.220 Chirality : 0.046 0.146 2176 Planarity : 0.003 0.037 2372 Dihedral : 3.187 14.216 1942 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.16 % Allowed : 20.76 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1760 helix: 0.72 (0.20), residues: 784 sheet: 0.28 (0.27), residues: 304 loop : -0.78 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.008 0.001 TYR C 333 PHE 0.006 0.001 PHE E 251 TRP 0.002 0.000 TRP E 123 HIS 0.004 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 (13444) covalent geometry : angle 0.42611 / 0.22 (18208) hydrogen bonds : bond 0.02955 / 2.07 ( 597) hydrogen bonds : angle 4.05358 / 2.87 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3281.60 seconds wall clock time: 56 minutes 50.61 seconds (3410.61 seconds total)