Starting phenix.real_space_refine on Thu Jul 31 07:32:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u5p_20652/07_2025/6u5p_20652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5p_20652/07_2025/6u5p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6u5p_20652/07_2025/6u5p_20652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5p_20652/07_2025/6u5p_20652.map" model { file = "/net/cci-nas-00/data/ceres_data/6u5p_20652/07_2025/6u5p_20652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5p_20652/07_2025/6u5p_20652.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 5, 'ARG:plan': 1, '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, 'ARG:plan': 3, 'ASP:plan': 4} 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, 'ASP:plan': 3, 'ARG:plan': 2} 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: {'GLU:plan': 5, 'ARG:plan': 1, '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, 'ARG:plan': 3, 'ASP:plan': 4} 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, 'ASP:plan': 3, 'ARG:plan': 2} 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: 7.93, per 1000 atoms: 0.60 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: 3.08 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.67 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: 3.81 Time building geometry restraints manager: 3.64 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: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.870 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.870 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.001 TRP B 123 HIS 0.014 0.002 HIS E 193 PHE 0.009 0.001 PHE E 251 TYR 0.011 0.002 TYR G 247 ARG 0.003 0.001 ARG G 298 Details of bonding type rmsd hydrogen bonds : bond 0.18294 ( 597) hydrogen bonds : angle 6.91270 ( 1707) covalent geometry : bond 0.00581 (13444) covalent geometry : angle 0.74996 (18208) *********************** 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 : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7459 (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: 0.7603 (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: 0.8096 (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: 0.3524 time to fit residues: 151.6715 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 : 1.473 ------------------------------------------------------------------------------- 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 148 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 219 GLN G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.154252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.115838 restraints weight = 14292.916| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.03 r_work: 0.2956 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13444 Z= 0.117 Angle : 0.460 4.662 18208 Z= 0.249 Chirality : 0.047 0.173 2176 Planarity : 0.004 0.027 2372 Dihedral : 4.242 28.234 1954 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.08 % Allowed : 13.29 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 1760 helix: -1.08 (0.17), residues: 776 sheet: 0.54 (0.26), residues: 304 loop : -2.03 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 123 HIS 0.005 0.001 HIS E 193 PHE 0.005 0.001 PHE G 251 TYR 0.007 0.001 TYR D 247 ARG 0.003 0.000 ARG H 298 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 597) hydrogen bonds : angle 4.74740 ( 1707) covalent geometry : bond 0.00275 (13444) covalent geometry : angle 0.45964 (18208) *********************** 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: 15 poor density : 249 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7593 (mtt180) cc_final: 0.6945 (mtm-85) REVERT: A 222 MET cc_start: 0.7084 (ptt) cc_final: 0.6800 (mtp) REVERT: A 333 TYR cc_start: 0.7476 (t80) cc_final: 0.6882 (t80) REVERT: E 154 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7920 (mtm-85) REVERT: E 190 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7973 (mt-10) REVERT: E 303 ILE cc_start: 0.8234 (mt) cc_final: 0.7715 (mm) REVERT: E 310 TYR cc_start: 0.7521 (t80) cc_final: 0.6785 (t80) REVERT: B 132 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7696 (ttm170) REVERT: B 212 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7659 (mp0) REVERT: B 213 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8321 (ttm170) REVERT: B 239 MET cc_start: 0.8986 (mtm) cc_final: 0.8738 (mtm) REVERT: C 132 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6920 (mtm-85) REVERT: C 333 TYR cc_start: 0.7467 (t80) cc_final: 0.6879 (t80) REVERT: G 154 ARG cc_start: 0.8378 (ttp-110) cc_final: 0.7962 (mtm-85) REVERT: G 190 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7961 (mt-10) REVERT: G 303 ILE cc_start: 0.8245 (mt) cc_final: 0.7731 (mm) REVERT: G 310 TYR cc_start: 0.7503 (t80) cc_final: 0.6754 (t80) REVERT: D 132 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7668 (ttm170) REVERT: D 212 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7665 (mp0) REVERT: D 213 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8320 (ttm170) REVERT: D 239 MET cc_start: 0.8996 (mtm) cc_final: 0.8754 (mtm) REVERT: H 303 ILE cc_start: 0.8039 (mt) cc_final: 0.7819 (mm) outliers start: 15 outliers final: 11 residues processed: 258 average time/residue: 0.3298 time to fit residues: 114.1329 Evaluate side-chains 256 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 243 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 132 ARG 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 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 3 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 158 optimal weight: 0.2980 chunk 110 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.153594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.114346 restraints weight = 14537.772| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.06 r_work: 0.2935 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1741 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= 0.123 Angle : 0.435 5.148 18208 Z= 0.232 Chirality : 0.047 0.152 2176 Planarity : 0.003 0.026 2372 Dihedral : 3.536 12.414 1942 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.65 % Allowed : 15.30 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 1760 helix: -0.27 (0.19), residues: 784 sheet: 0.41 (0.26), residues: 304 loop : -1.61 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 123 HIS 0.006 0.001 HIS E 193 PHE 0.003 0.001 PHE A 312 TYR 0.006 0.001 TYR D 247 ARG 0.003 0.000 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 597) hydrogen bonds : angle 4.35729 ( 1707) covalent geometry : bond 0.00300 (13444) covalent geometry : angle 0.43506 (18208) *********************** 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 275 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7642 (mtt180) cc_final: 0.6996 (mtm-85) REVERT: A 222 MET cc_start: 0.6996 (ptt) cc_final: 0.6759 (mtp) REVERT: A 245 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7161 (p0) REVERT: A 247 TYR cc_start: 0.8799 (m-80) cc_final: 0.7939 (m-80) REVERT: A 333 TYR cc_start: 0.7532 (t80) cc_final: 0.7057 (t80) REVERT: E 154 ARG cc_start: 0.8405 (ttp-110) cc_final: 0.8089 (mtm-85) REVERT: E 190 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7919 (mt-10) REVERT: E 303 ILE cc_start: 0.8119 (mt) cc_final: 0.7622 (mm) REVERT: B 212 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7736 (mp0) REVERT: B 213 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8318 (ttm170) REVERT: B 239 MET cc_start: 0.8989 (mtm) cc_final: 0.8753 (mtm) REVERT: F 188 ASP cc_start: 0.8093 (t0) cc_final: 0.7869 (t0) REVERT: F 301 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: C 132 ARG cc_start: 0.7620 (mtt180) cc_final: 0.6967 (mtm-85) REVERT: C 247 TYR cc_start: 0.8779 (m-80) cc_final: 0.7903 (m-80) REVERT: C 333 TYR cc_start: 0.7535 (t80) cc_final: 0.7064 (t80) REVERT: G 154 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8090 (mtm-85) REVERT: G 190 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7916 (mt-10) REVERT: G 303 ILE cc_start: 0.8093 (mt) cc_final: 0.7618 (mm) REVERT: D 212 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7727 (mp0) REVERT: D 213 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8315 (ttm170) REVERT: D 239 MET cc_start: 0.8998 (mtm) cc_final: 0.8759 (mtm) REVERT: D 321 ILE cc_start: 0.9069 (mt) cc_final: 0.8744 (mt) REVERT: H 301 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6580 (pm20) REVERT: H 303 ILE cc_start: 0.8082 (mt) cc_final: 0.7831 (mm) outliers start: 23 outliers final: 17 residues processed: 266 average time/residue: 0.3419 time to fit residues: 121.5096 Evaluate side-chains 263 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 E residue 244 ASP Chi-restraints excluded: chain E residue 267 VAL 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 248 GLU 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 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 248 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 30 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.150586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.112587 restraints weight = 14368.557| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.05 r_work: 0.2905 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13444 Z= 0.198 Angle : 0.489 4.982 18208 Z= 0.258 Chirality : 0.049 0.159 2176 Planarity : 0.004 0.032 2372 Dihedral : 3.701 14.828 1942 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.37 % Allowed : 17.74 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1760 helix: -0.12 (0.19), residues: 784 sheet: 0.20 (0.25), residues: 304 loop : -1.52 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 123 HIS 0.010 0.002 HIS E 193 PHE 0.006 0.001 PHE A 232 TYR 0.007 0.001 TYR B 247 ARG 0.003 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 597) hydrogen bonds : angle 4.37116 ( 1707) covalent geometry : bond 0.00498 (13444) covalent geometry : angle 0.48936 (18208) *********************** 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 278 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7323 (mtm-85) REVERT: A 222 MET cc_start: 0.7082 (ptt) cc_final: 0.6854 (mtp) REVERT: A 313 ARG cc_start: 0.5052 (mtm-85) cc_final: 0.4839 (mtm-85) REVERT: A 333 TYR cc_start: 0.7541 (t80) cc_final: 0.7036 (t80) REVERT: E 154 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8110 (mtm-85) REVERT: E 303 ILE cc_start: 0.8225 (mt) cc_final: 0.7677 (mm) REVERT: E 310 TYR cc_start: 0.7445 (t80) cc_final: 0.6660 (t80) REVERT: B 171 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: B 212 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7835 (mp0) REVERT: B 213 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8400 (ttm170) REVERT: B 305 ASP cc_start: 0.8300 (t70) cc_final: 0.8035 (t70) REVERT: C 132 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7358 (mtm-85) REVERT: C 333 TYR cc_start: 0.7549 (t80) cc_final: 0.7031 (t80) REVERT: G 154 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.8071 (mtm-85) REVERT: G 303 ILE cc_start: 0.8222 (mt) cc_final: 0.7690 (mm) REVERT: G 310 TYR cc_start: 0.7404 (t80) cc_final: 0.6611 (t80) REVERT: D 171 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: D 212 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7837 (mp0) REVERT: D 213 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8407 (ttm170) REVERT: D 305 ASP cc_start: 0.8320 (t70) cc_final: 0.8046 (t70) REVERT: H 303 ILE cc_start: 0.8186 (mt) cc_final: 0.7922 (mm) outliers start: 33 outliers final: 24 residues processed: 266 average time/residue: 0.3290 time to fit residues: 117.5699 Evaluate side-chains 257 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL 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 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 248 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain G residue 244 ASP 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 248 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.153412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.115615 restraints weight = 14415.190| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.79 r_work: 0.2994 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13444 Z= 0.099 Angle : 0.420 8.791 18208 Z= 0.221 Chirality : 0.046 0.143 2176 Planarity : 0.003 0.027 2372 Dihedral : 3.386 13.260 1942 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.37 % Allowed : 18.03 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 1760 helix: 0.30 (0.20), residues: 776 sheet: 0.20 (0.25), residues: 304 loop : -1.31 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.004 0.000 HIS E 193 PHE 0.003 0.001 PHE C 312 TYR 0.008 0.001 TYR A 333 ARG 0.003 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 597) hydrogen bonds : angle 4.19577 ( 1707) covalent geometry : bond 0.00239 (13444) covalent geometry : angle 0.42045 (18208) *********************** 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 278 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7092 (mtm-85) REVERT: A 245 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6754 (p0) REVERT: A 247 TYR cc_start: 0.8793 (m-80) cc_final: 0.7923 (m-80) REVERT: A 333 TYR cc_start: 0.7508 (t80) cc_final: 0.7106 (t80) REVERT: E 154 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8105 (mtm-85) REVERT: E 303 ILE cc_start: 0.8172 (mt) cc_final: 0.7694 (mm) REVERT: B 213 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8278 (ttm170) REVERT: F 188 ASP cc_start: 0.8010 (t0) cc_final: 0.7809 (t0) REVERT: F 241 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7703 (mtp85) REVERT: F 285 ILE cc_start: 0.7581 (mm) cc_final: 0.7245 (mm) REVERT: C 132 ARG cc_start: 0.7598 (mtt180) cc_final: 0.6974 (mtm-85) REVERT: C 247 TYR cc_start: 0.8761 (m-80) cc_final: 0.7944 (m-80) REVERT: C 333 TYR cc_start: 0.7509 (t80) cc_final: 0.7099 (t80) REVERT: G 154 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8091 (mtm-85) REVERT: G 190 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7766 (mt-10) REVERT: G 303 ILE cc_start: 0.8158 (mt) cc_final: 0.7692 (mm) REVERT: D 213 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8275 (ttm170) REVERT: D 305 ASP cc_start: 0.8191 (t70) cc_final: 0.7930 (t70) REVERT: H 241 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7695 (mtp85) REVERT: H 285 ILE cc_start: 0.7577 (mm) cc_final: 0.7248 (mm) outliers start: 33 outliers final: 23 residues processed: 262 average time/residue: 0.3386 time to fit residues: 119.2009 Evaluate side-chains 254 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 F residue 187 SER Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain C residue 205 VAL 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 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 H residue 215 GLU Chi-restraints excluded: chain H residue 248 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 137 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.152760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.114691 restraints weight = 14483.356| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.06 r_work: 0.2934 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2175 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= 0.120 Angle : 0.443 11.475 18208 Z= 0.228 Chirality : 0.047 0.150 2176 Planarity : 0.003 0.041 2372 Dihedral : 3.342 13.444 1942 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.44 % Allowed : 18.82 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1760 helix: 0.42 (0.20), residues: 776 sheet: 0.24 (0.25), residues: 304 loop : -1.20 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.005 0.001 HIS G 193 PHE 0.007 0.001 PHE G 251 TYR 0.010 0.001 TYR G 310 ARG 0.004 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 597) hydrogen bonds : angle 4.17116 ( 1707) covalent geometry : bond 0.00296 (13444) covalent geometry : angle 0.44264 (18208) *********************** 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 267 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7334 (mtm-85) REVERT: A 247 TYR cc_start: 0.8863 (m-80) cc_final: 0.8124 (m-80) REVERT: A 333 TYR cc_start: 0.7573 (t80) cc_final: 0.7161 (t80) REVERT: E 154 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8112 (mtm-85) REVERT: E 190 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7905 (mt-10) REVERT: E 303 ILE cc_start: 0.8276 (mt) cc_final: 0.7743 (mm) REVERT: B 132 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7843 (ttm170) REVERT: B 213 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8370 (ttm170) REVERT: F 153 LEU cc_start: 0.7040 (mp) cc_final: 0.6752 (mp) REVERT: F 241 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7788 (mtp85) REVERT: F 285 ILE cc_start: 0.7715 (mm) cc_final: 0.7390 (mm) REVERT: C 132 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7326 (mtm-85) REVERT: C 247 TYR cc_start: 0.8858 (m-80) cc_final: 0.8015 (m-80) REVERT: C 333 TYR cc_start: 0.7566 (t80) cc_final: 0.7154 (t80) REVERT: G 154 ARG cc_start: 0.8439 (ttp-110) cc_final: 0.8110 (mtm-85) REVERT: G 190 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7905 (mt-10) REVERT: G 303 ILE cc_start: 0.8286 (mt) cc_final: 0.7749 (mm) REVERT: D 213 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8373 (ttm170) REVERT: H 153 LEU cc_start: 0.7049 (mp) cc_final: 0.6758 (mp) REVERT: H 241 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7769 (mtp85) REVERT: H 285 ILE cc_start: 0.7745 (mm) cc_final: 0.7423 (mm) outliers start: 34 outliers final: 26 residues processed: 254 average time/residue: 0.3388 time to fit residues: 115.4307 Evaluate side-chains 242 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL 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 267 VAL Chi-restraints excluded: chain B residue 132 ARG 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 248 GLU 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 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 248 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.150811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.113166 restraints weight = 14503.670| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.77 r_work: 0.2962 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13444 Z= 0.172 Angle : 0.471 7.044 18208 Z= 0.245 Chirality : 0.048 0.148 2176 Planarity : 0.003 0.039 2372 Dihedral : 3.516 14.037 1942 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.30 % Allowed : 19.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 1760 helix: 0.30 (0.19), residues: 784 sheet: 0.19 (0.26), residues: 304 loop : -1.11 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 123 HIS 0.007 0.001 HIS E 193 PHE 0.007 0.001 PHE G 251 TYR 0.009 0.001 TYR E 310 ARG 0.005 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 597) hydrogen bonds : angle 4.23425 ( 1707) covalent geometry : bond 0.00433 (13444) covalent geometry : angle 0.47090 (18208) *********************** 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 260 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7297 (mtm-85) REVERT: A 247 TYR cc_start: 0.8811 (m-80) cc_final: 0.8053 (m-80) REVERT: A 333 TYR cc_start: 0.7496 (t80) cc_final: 0.7101 (t80) REVERT: E 154 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.8113 (mtm-85) REVERT: E 190 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7759 (mt-10) REVERT: E 303 ILE cc_start: 0.8112 (mt) cc_final: 0.7574 (mm) REVERT: B 132 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7597 (ttm170) REVERT: B 213 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8278 (ttm170) REVERT: B 305 ASP cc_start: 0.8154 (t70) cc_final: 0.7872 (t70) REVERT: F 285 ILE cc_start: 0.7682 (mm) cc_final: 0.7422 (mm) REVERT: C 132 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7282 (mtm-85) REVERT: C 247 TYR cc_start: 0.8805 (m-80) cc_final: 0.8079 (m-80) REVERT: C 333 TYR cc_start: 0.7487 (t80) cc_final: 0.7093 (t80) REVERT: G 154 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8113 (mtm-85) REVERT: G 190 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7783 (mt-10) REVERT: G 303 ILE cc_start: 0.8120 (mt) cc_final: 0.7582 (mm) REVERT: D 213 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8286 (ttm170) REVERT: D 305 ASP cc_start: 0.8146 (t70) cc_final: 0.7862 (t70) REVERT: H 285 ILE cc_start: 0.7697 (mm) cc_final: 0.7440 (mm) outliers start: 32 outliers final: 25 residues processed: 249 average time/residue: 0.3661 time to fit residues: 120.7447 Evaluate side-chains 244 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL 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 267 VAL Chi-restraints excluded: chain B residue 132 ARG 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 248 GLU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 51 optimal weight: 0.0170 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.151641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.113519 restraints weight = 14510.611| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.99 r_work: 0.2927 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13444 Z= 0.135 Angle : 0.451 7.290 18208 Z= 0.235 Chirality : 0.047 0.151 2176 Planarity : 0.003 0.034 2372 Dihedral : 3.422 14.101 1942 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.37 % Allowed : 19.76 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 1760 helix: 0.47 (0.20), residues: 776 sheet: 0.15 (0.26), residues: 304 loop : -1.05 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 123 HIS 0.005 0.001 HIS E 193 PHE 0.006 0.001 PHE G 251 TYR 0.009 0.001 TYR E 310 ARG 0.004 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 597) hydrogen bonds : angle 4.19483 ( 1707) covalent geometry : bond 0.00339 (13444) covalent geometry : angle 0.45051 (18208) *********************** 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 254 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7402 (mtm-85) REVERT: A 203 GLU cc_start: 0.8197 (tp30) cc_final: 0.7833 (tp30) REVERT: A 247 TYR cc_start: 0.8878 (m-80) cc_final: 0.8173 (m-80) REVERT: A 333 TYR cc_start: 0.7545 (t80) cc_final: 0.7093 (t80) REVERT: E 154 ARG cc_start: 0.8521 (ttp-110) cc_final: 0.8159 (mtm-85) REVERT: E 190 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7912 (mt-10) REVERT: E 303 ILE cc_start: 0.8244 (mt) cc_final: 0.7684 (mm) REVERT: B 132 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7748 (ttm170) REVERT: B 213 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8391 (ttm170) REVERT: C 132 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7368 (mtm-85) REVERT: C 247 TYR cc_start: 0.8866 (m-80) cc_final: 0.8163 (m-80) REVERT: C 333 TYR cc_start: 0.7531 (t80) cc_final: 0.7080 (t80) REVERT: G 154 ARG cc_start: 0.8518 (ttp-110) cc_final: 0.8158 (mtm-85) REVERT: G 190 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7925 (mt-10) REVERT: G 303 ILE cc_start: 0.8248 (mt) cc_final: 0.7708 (mm) REVERT: D 213 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.8393 (ttm170) outliers start: 33 outliers final: 28 residues processed: 243 average time/residue: 0.3806 time to fit residues: 125.4095 Evaluate side-chains 243 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain B residue 132 ARG 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 184 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 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 20 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 89 optimal weight: 0.7980 chunk 169 optimal weight: 0.1980 chunk 166 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.152524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.114535 restraints weight = 14336.689| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.01 r_work: 0.2937 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13444 Z= 0.112 Angle : 0.438 6.993 18208 Z= 0.228 Chirality : 0.047 0.149 2176 Planarity : 0.003 0.039 2372 Dihedral : 3.327 14.041 1942 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.23 % Allowed : 20.47 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1760 helix: 0.58 (0.20), residues: 776 sheet: 0.17 (0.26), residues: 304 loop : -0.97 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.004 0.001 HIS E 193 PHE 0.006 0.001 PHE E 251 TYR 0.008 0.001 TYR A 333 ARG 0.005 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 597) hydrogen bonds : angle 4.14713 ( 1707) covalent geometry : bond 0.00276 (13444) covalent geometry : angle 0.43796 (18208) *********************** 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 242 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7251 (mtm-85) REVERT: A 247 TYR cc_start: 0.8806 (m-80) cc_final: 0.8097 (m-80) REVERT: A 333 TYR cc_start: 0.7559 (t80) cc_final: 0.7057 (t80) REVERT: E 154 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8221 (mtm-85) REVERT: E 190 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7858 (mt-10) REVERT: E 303 ILE cc_start: 0.8198 (mt) cc_final: 0.7661 (mm) REVERT: B 132 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7828 (ttm170) REVERT: B 213 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8335 (ttm170) REVERT: C 132 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7243 (mtm-85) REVERT: C 247 TYR cc_start: 0.8796 (m-80) cc_final: 0.8081 (m-80) REVERT: C 333 TYR cc_start: 0.7509 (t80) cc_final: 0.6975 (t80) REVERT: G 154 ARG cc_start: 0.8516 (ttp-110) cc_final: 0.8227 (mtm-85) REVERT: G 190 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7865 (mt-10) REVERT: G 303 ILE cc_start: 0.8204 (mt) cc_final: 0.7663 (mm) REVERT: D 213 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8337 (ttm170) outliers start: 31 outliers final: 27 residues processed: 230 average time/residue: 0.3970 time to fit residues: 122.4616 Evaluate side-chains 233 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain B residue 132 ARG 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 184 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 139 VAL Chi-restraints excluded: chain G residue 244 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 143 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 161 optimal weight: 0.0270 chunk 163 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.152963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.115408 restraints weight = 14414.085| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.78 r_work: 0.2991 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13444 Z= 0.106 Angle : 0.432 5.810 18208 Z= 0.226 Chirality : 0.047 0.159 2176 Planarity : 0.003 0.040 2372 Dihedral : 3.273 14.139 1942 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.16 % Allowed : 20.62 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1760 helix: 0.65 (0.20), residues: 776 sheet: 0.16 (0.26), residues: 304 loop : -0.91 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 123 HIS 0.004 0.001 HIS E 193 PHE 0.006 0.001 PHE E 251 TYR 0.008 0.001 TYR C 333 ARG 0.005 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 597) hydrogen bonds : angle 4.12619 ( 1707) covalent geometry : bond 0.00263 (13444) covalent geometry : angle 0.43166 (18208) ********************** 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 243 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7194 (mtm-85) REVERT: A 247 TYR cc_start: 0.8736 (m-80) cc_final: 0.7911 (m-80) REVERT: A 333 TYR cc_start: 0.7470 (t80) cc_final: 0.6986 (t80) REVERT: E 154 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8217 (mtm-85) REVERT: E 190 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 303 ILE cc_start: 0.8120 (mt) cc_final: 0.7585 (mm) REVERT: B 132 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7754 (ttm170) REVERT: B 213 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8273 (ttm170) REVERT: F 132 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7616 (ttp80) REVERT: F 285 ILE cc_start: 0.7706 (mm) cc_final: 0.7381 (mm) REVERT: C 132 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7166 (mtm-85) REVERT: C 247 TYR cc_start: 0.8732 (m-80) cc_final: 0.8027 (m-80) REVERT: C 333 TYR cc_start: 0.7459 (t80) cc_final: 0.6974 (t80) REVERT: G 154 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8224 (mtm-85) REVERT: G 190 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7736 (mt-10) REVERT: G 303 ILE cc_start: 0.8117 (mt) cc_final: 0.7586 (mm) REVERT: D 213 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8277 (ttm170) REVERT: H 132 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7598 (ttp80) outliers start: 30 outliers final: 28 residues processed: 234 average time/residue: 0.3680 time to fit residues: 115.7551 Evaluate side-chains 243 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain B residue 132 ARG 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 184 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 139 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 170 optimal weight: 8.9990 chunk 95 optimal weight: 0.1980 chunk 150 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.153559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.115677 restraints weight = 14434.134| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.03 r_work: 0.2952 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13444 Z= 0.094 Angle : 0.427 8.272 18208 Z= 0.221 Chirality : 0.046 0.147 2176 Planarity : 0.003 0.041 2372 Dihedral : 3.193 13.989 1942 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.23 % Allowed : 20.83 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1760 helix: 0.75 (0.20), residues: 776 sheet: 0.20 (0.27), residues: 304 loop : -0.85 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 123 HIS 0.003 0.000 HIS E 193 PHE 0.006 0.001 PHE E 251 TYR 0.008 0.001 TYR A 333 ARG 0.004 0.000 ARG F 241 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 597) hydrogen bonds : angle 4.11070 ( 1707) covalent geometry : bond 0.00230 (13444) covalent geometry : angle 0.42658 (18208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7445.90 seconds wall clock time: 131 minutes 42.99 seconds (7902.99 seconds total)