Starting phenix.real_space_refine on Thu Jul 2 20:56:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uxb_20932/07_2026/6uxb_20932.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uxb_20932/07_2026/6uxb_20932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uxb_20932/07_2026/6uxb_20932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uxb_20932/07_2026/6uxb_20932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uxb_20932/07_2026/6uxb_20932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uxb_20932/07_2026/6uxb_20932.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 6136 2.51 5 N 2104 2.21 5 O 2104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10344 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'ARG:plan': 22, 'TYR:plan': 9, 'PHE:plan': 11, 'HIS:plan': 5, 'GLU:plan': 28, 'TRP:plan': 3, 'ASP:plan': 18, 'ASN:plan1': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 484 Chain: "E" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 20, 'HIS:plan': 4, 'TRP:plan': 1, 'GLU:plan': 24, 'PHE:plan': 5, 'ASP:plan': 17, 'ASN:plan1': 5, 'TYR:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 361 Chain: "C" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'ARG:plan': 22, 'TYR:plan': 9, 'PHE:plan': 11, 'HIS:plan': 5, 'GLU:plan': 28, 'TRP:plan': 3, 'ASP:plan': 18, 'ASN:plan1': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 484 Chain: "G" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 20, 'HIS:plan': 4, 'TRP:plan': 1, 'GLU:plan': 24, 'PHE:plan': 5, 'ASP:plan': 17, 'ASN:plan1': 5, 'TYR:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 361 Chain: "B" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'ARG:plan': 22, 'TYR:plan': 9, 'PHE:plan': 11, 'HIS:plan': 5, 'GLU:plan': 28, 'TRP:plan': 3, 'ASP:plan': 18, 'ASN:plan1': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 484 Chain: "F" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 20, 'HIS:plan': 4, 'TRP:plan': 1, 'GLU:plan': 24, 'PHE:plan': 5, 'ASP:plan': 17, 'ASN:plan1': 5, 'TYR:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 361 Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'ARG:plan': 22, 'TYR:plan': 9, 'PHE:plan': 11, 'HIS:plan': 5, 'GLU:plan': 28, 'TRP:plan': 3, 'ASP:plan': 18, 'ASN:plan1': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 484 Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 20, 'HIS:plan': 4, 'TRP:plan': 1, 'GLU:plan': 24, 'PHE:plan': 5, 'ASP:plan': 17, 'ASN:plan1': 5, 'TYR:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 361 Time building chain proxies: 2.46, per 1000 atoms: 0.24 Number of scatterers: 10344 At special positions: 0 Unit cell: (140.17, 139.1, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2104 8.00 N 2104 7.00 C 6136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 572.7 milliseconds 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 51.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 19 through 43 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 69 through 99 removed outlier: 4.893A pdb=" N GLY A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) 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: 3.806A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.536A 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: 3.500A 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: 3.705A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.648A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.586A 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: 3.549A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 3.564A 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 'C' and resid 19 through 43 Processing helix chain 'C' and resid 45 through 58 Processing helix chain 'C' and resid 69 through 99 removed outlier: 4.893A pdb=" N GLY C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) 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: 3.808A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.536A 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: 3.811A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.704A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.647A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.587A 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: 3.747A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.563A 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 'B' and resid 19 through 43 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 69 through 99 removed outlier: 4.894A pdb=" N GLY B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) 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: 3.790A 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: 3.692A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.530A 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: 3.710A 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: 3.566A 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: 3.584A 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 'D' and resid 19 through 43 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'D' and resid 69 through 99 removed outlier: 4.893A pdb=" N GLY D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) 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: 3.789A 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: 3.693A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.530A 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: 3.940A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.708A 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: 3.787A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.600A 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: 7.174A 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: 6.623A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.620A 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: 7.390A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.686A 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: 7.535A pdb=" N VAL E 160 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL E 141 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.493A 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: 5.600A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.407A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.623A 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: 6.476A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 268 removed outlier: 7.389A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AA7, 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: 6.385A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.060A 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: 6.906A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.960A 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=AA8, 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=AA9, 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: 6.412A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.735A 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: 4.213A 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: 6.447A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.598A 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: 7.909A 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=AB1, 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: 5.670A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB2, 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: 7.290A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 263 through 268 removed outlier: 7.231A 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=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.550A 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: 6.411A 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: 6.076A pdb=" N HIS D 117 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 180 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE D 208 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.447A 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: 7.601A 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: 7.238A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.671A 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: 7.231A 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) 814 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 2104 1.28 - 1.36: 2092 1.36 - 1.43: 0 1.43 - 1.51: 2113 1.51 - 1.58: 4023 Bond restraints: 10332 Sorted by residual: bond pdb=" C VAL D 60 " pdb=" O VAL D 60 " ideal model delta sigma weight residual 1.237 1.268 -0.031 1.12e-02 7.97e+03 7.77e+00 bond pdb=" C VAL A 60 " pdb=" O VAL A 60 " ideal model delta sigma weight residual 1.237 1.268 -0.031 1.12e-02 7.97e+03 7.72e+00 bond pdb=" CA VAL A 55 " pdb=" CB VAL A 55 " ideal model delta sigma weight residual 1.542 1.580 -0.039 1.45e-02 4.76e+03 7.16e+00 bond pdb=" CA VAL B 55 " pdb=" CB VAL B 55 " ideal model delta sigma weight residual 1.542 1.579 -0.037 1.45e-02 4.76e+03 6.68e+00 bond pdb=" C VAL C 60 " pdb=" O VAL C 60 " ideal model delta sigma weight residual 1.237 1.265 -0.029 1.12e-02 7.97e+03 6.62e+00 ... (remaining 10327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 11941 0.94 - 1.89: 1968 1.89 - 2.83: 313 2.83 - 3.77: 90 3.77 - 4.72: 28 Bond angle restraints: 14340 Sorted by residual: angle pdb=" C SER D 66 " pdb=" N PRO D 67 " pdb=" CA PRO D 67 " ideal model delta sigma weight residual 119.76 116.58 3.18 1.00e+00 1.00e+00 1.01e+01 angle pdb=" C SER C 66 " pdb=" N PRO C 67 " pdb=" CA PRO C 67 " ideal model delta sigma weight residual 119.76 116.60 3.16 1.00e+00 1.00e+00 1.00e+01 angle pdb=" C SER B 66 " pdb=" N PRO B 67 " pdb=" CA PRO B 67 " ideal model delta sigma weight residual 119.76 116.62 3.14 1.00e+00 1.00e+00 9.87e+00 angle pdb=" N GLU D 171 " pdb=" CA GLU D 171 " pdb=" C GLU D 171 " ideal model delta sigma weight residual 111.28 114.66 -3.38 1.09e+00 8.42e-01 9.64e+00 angle pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 111.28 114.65 -3.37 1.09e+00 8.42e-01 9.58e+00 ... (remaining 14335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.04: 4797 3.04 - 6.07: 770 6.07 - 9.11: 258 9.11 - 12.14: 95 12.14 - 15.18: 28 Dihedral angle restraints: 5948 sinusoidal: 0 harmonic: 5948 Sorted by residual: dihedral pdb=" C VAL B 27 " pdb=" N VAL B 27 " pdb=" CA VAL B 27 " pdb=" CB VAL B 27 " ideal model delta harmonic sigma weight residual -122.00 -131.33 9.33 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" C VAL C 27 " pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" CB VAL C 27 " ideal model delta harmonic sigma weight residual -122.00 -131.22 9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C VAL D 27 " pdb=" N VAL D 27 " pdb=" CA VAL D 27 " pdb=" CB VAL D 27 " ideal model delta harmonic sigma weight residual -122.00 -131.15 9.15 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1361 0.060 - 0.119: 443 0.119 - 0.179: 110 0.179 - 0.238: 10 0.238 - 0.298: 4 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CA THR B 59 " pdb=" N THR B 59 " pdb=" C THR B 59 " pdb=" CB THR B 59 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA THR C 59 " pdb=" N THR C 59 " pdb=" C THR C 59 " pdb=" CB THR C 59 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA THR A 59 " pdb=" N THR A 59 " pdb=" C THR A 59 " pdb=" CB THR A 59 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1925 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 169 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.39e+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 ASP D 169 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+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 VAL B 267 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+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 " 0.011 2.00e-02 2.50e+03 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 6537 3.09 - 3.54: 10951 3.54 - 3.99: 12163 3.99 - 4.45: 13953 4.45 - 4.90: 22647 Nonbonded interactions: 66251 Sorted by model distance: nonbonded pdb=" N GLY E 136 " pdb=" N SER E 137 " model vdw 2.637 2.560 nonbonded pdb=" N GLY G 136 " pdb=" N SER G 137 " model vdw 2.639 2.560 nonbonded pdb=" N SER D 66 " pdb=" O SER D 66 " model vdw 2.640 2.496 nonbonded pdb=" N SER B 66 " pdb=" O SER B 66 " model vdw 2.641 2.496 nonbonded pdb=" N VAL D 181 " pdb=" O ARG D 206 " model vdw 2.642 3.120 ... (remaining 66246 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 : 0.005 0.041 10332 Z= 0.340 Angle : 0.775 4.717 14340 Z= 0.537 Chirality : 0.062 0.298 1928 Planarity : 0.004 0.029 2092 Dihedral : 4.562 15.179 2092 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.15), residues: 2080 helix: -1.92 (0.13), residues: 1080 sheet: 0.64 (0.25), residues: 336 loop : -2.29 (0.17), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.34 (10332) covalent geometry : angle 0.77489 / 0.54 (14340) hydrogen bonds : bond 0.16820 / 12.75 ( 814) hydrogen bonds : angle 6.99762 / 5.34 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0106 time to fit residues: 0.1637 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.059 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0064 time to fit residues: 0.1006 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.089848 restraints weight = 7375.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090505 restraints weight = 6817.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091109 restraints weight = 6343.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091548 restraints weight = 5962.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091549 restraints weight = 5656.564| |-----------------------------------------------------------------------------| r_work (final): 0.3321 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.060027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.050234 restraints weight = 7407.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.050968 restraints weight = 5830.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.051750 restraints weight = 4855.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.052205 restraints weight = 4130.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.052648 restraints weight = 3639.641| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 1.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10332 Z= 0.353 Angle : 0.685 5.381 14340 Z= 0.469 Chirality : 0.048 0.242 1928 Planarity : 0.005 0.026 2092 Dihedral : 5.422 32.977 2092 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2080 helix: 0.00 (0.16), residues: 1032 sheet: 1.09 (0.25), residues: 340 loop : -1.26 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.35 (10332) covalent geometry : angle 0.68454 / 0.47 (14340) hydrogen bonds : bond 0.05208 / 4.03 ( 814) hydrogen bonds : angle 5.70618 / 4.34 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0059 time to fit residues: 0.1173 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.051 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0067 time to fit residues: 0.1119 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 16 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 111 optimal weight: 50.0000 chunk 81 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 186 optimal weight: 0.0370 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 overall best weight: 4.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093427 restraints weight = 7283.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094084 restraints weight = 6675.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.094804 restraints weight = 6210.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094848 restraints weight = 5823.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094849 restraints weight = 5786.821| |-----------------------------------------------------------------------------| r_work (final): 0.3367 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.058892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.049259 restraints weight = 7585.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.050088 restraints weight = 5988.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.050771 restraints weight = 4943.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.051368 restraints weight = 4203.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.051776 restraints weight = 3659.420| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 1.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 10332 Z= 0.206 Angle : 0.456 3.494 14340 Z= 0.304 Chirality : 0.048 0.182 1928 Planarity : 0.003 0.015 2092 Dihedral : 3.662 15.694 2092 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2080 helix: 1.23 (0.17), residues: 1068 sheet: 1.33 (0.28), residues: 312 loop : -0.21 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.21 (10332) covalent geometry : angle 0.45585 / 0.30 (14340) hydrogen bonds : bond 0.02864 / 2.20 ( 814) hydrogen bonds : angle 4.58008 / 3.49 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.058 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0064 time to fit residues: 0.1285 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.039 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0053 time to fit residues: 0.0779 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 51 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 152 optimal weight: 40.0000 chunk 62 optimal weight: 0.0010 chunk 173 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.121620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100905 restraints weight = 7047.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101610 restraints weight = 6486.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101631 restraints weight = 6031.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101631 restraints weight = 6014.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101631 restraints weight = 6014.843| |-----------------------------------------------------------------------------| r_work (final): 0.3466 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.055066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.046413 restraints weight = 8125.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.047151 restraints weight = 6380.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.047850 restraints weight = 5265.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.048284 restraints weight = 4444.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.048588 restraints weight = 3887.047| |-----------------------------------------------------------------------------| r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 1.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 10332 Z= 0.289 Angle : 0.545 4.411 14340 Z= 0.372 Chirality : 0.047 0.128 1928 Planarity : 0.003 0.015 2092 Dihedral : 4.501 14.555 2092 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2080 helix: 0.43 (0.15), residues: 1084 sheet: 0.85 (0.31), residues: 312 loop : -0.01 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.29 (10332) covalent geometry : angle 0.54464 / 0.37 (14340) hydrogen bonds : bond 0.04265 / 3.28 ( 814) hydrogen bonds : angle 5.57026 / 4.25 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0081 time to fit residues: 0.1550 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.053 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0066 time to fit residues: 0.1104 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 84 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 153 optimal weight: 40.0000 chunk 120 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 50 optimal weight: 0.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.125532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104820 restraints weight = 7122.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105494 restraints weight = 6616.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105965 restraints weight = 6196.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106664 restraints weight = 5877.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106678 restraints weight = 5578.369| |-----------------------------------------------------------------------------| r_work (final): 0.3534 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.055546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.046252 restraints weight = 7942.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.047164 restraints weight = 6114.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.047852 restraints weight = 4940.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.048459 restraints weight = 4138.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.048848 restraints weight = 3558.529| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 1.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 10332 Z= 0.230 Angle : 0.463 2.910 14340 Z= 0.314 Chirality : 0.046 0.134 1928 Planarity : 0.003 0.016 2092 Dihedral : 3.983 15.242 2092 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 2080 helix: 0.96 (0.16), residues: 1076 sheet: 0.78 (0.30), residues: 312 loop : 0.17 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.23 (10332) covalent geometry : angle 0.46295 / 0.31 (14340) hydrogen bonds : bond 0.03247 / 2.49 ( 814) hydrogen bonds : angle 5.13206 / 3.92 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.065 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0068 time to fit residues: 0.1454 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.065 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0085 time to fit residues: 0.1629 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 146 optimal weight: 0.7980 overall best weight: 9.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.080292 restraints weight = 7950.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080299 restraints weight = 7692.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080299 restraints weight = 7674.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080299 restraints weight = 7674.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080299 restraints weight = 7674.651| |-----------------------------------------------------------------------------| r_work (final): 0.3119 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.053001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.044386 restraints weight = 8166.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.045213 restraints weight = 6245.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.045926 restraints weight = 5019.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.046458 restraints weight = 4163.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.046843 restraints weight = 3560.110| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 1.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 10332 Z= 0.389 Angle : 0.600 4.126 14340 Z= 0.419 Chirality : 0.046 0.128 1928 Planarity : 0.004 0.020 2092 Dihedral : 4.834 14.412 2092 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2080 helix: -0.38 (0.14), residues: 1068 sheet: 0.20 (0.29), residues: 332 loop : -0.20 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.39 (10332) covalent geometry : angle 0.59998 / 0.42 (14340) hydrogen bonds : bond 0.04911 / 3.78 ( 814) hydrogen bonds : angle 6.33846 / 4.83 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0079 time to fit residues: 0.1323 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.055 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0042 time to fit residues: 0.0647 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 143 optimal weight: 0.0050 chunk 25 optimal weight: 20.0000 chunk 201 optimal weight: 0.1980 chunk 104 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 199 optimal weight: 0.7980 chunk 26 optimal weight: 50.0000 chunk 16 optimal weight: 10.0000 chunk 101 optimal weight: 40.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088063 restraints weight = 8738.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088063 restraints weight = 8674.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088063 restraints weight = 8674.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088063 restraints weight = 8674.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088063 restraints weight = 8674.485| |-----------------------------------------------------------------------------| r_work (final): 0.3187 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.055587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.046230 restraints weight = 7750.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.047104 restraints weight = 5982.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.047847 restraints weight = 4832.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.048428 restraints weight = 4036.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.048898 restraints weight = 3469.264| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 1.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.007 10332 Z= 0.129 Angle : 0.390 3.478 14340 Z= 0.256 Chirality : 0.047 0.128 1928 Planarity : 0.002 0.014 2092 Dihedral : 3.742 11.053 2092 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 2080 helix: 1.38 (0.16), residues: 1096 sheet: 0.57 (0.30), residues: 312 loop : -0.14 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.13 (10332) covalent geometry : angle 0.38956 / 0.26 (14340) hydrogen bonds : bond 0.02804 / 2.15 ( 814) hydrogen bonds : angle 4.77481 / 3.66 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0061 time to fit residues: 0.1052 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.055 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0064 time to fit residues: 0.1068 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 127 optimal weight: 40.0000 chunk 183 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 7 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 138 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 195 optimal weight: 0.6980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087322 restraints weight = 8661.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087322 restraints weight = 8538.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087322 restraints weight = 8538.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087322 restraints weight = 8538.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087322 restraints weight = 8538.424| |-----------------------------------------------------------------------------| r_work (final): 0.3181 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.055476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.046294 restraints weight = 7857.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.047120 restraints weight = 6053.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.047892 restraints weight = 4911.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.048395 restraints weight = 4096.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.048875 restraints weight = 3543.086| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 1.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 10332 Z= 0.141 Angle : 0.384 3.081 14340 Z= 0.254 Chirality : 0.046 0.130 1928 Planarity : 0.002 0.012 2092 Dihedral : 3.248 9.952 2092 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.20), residues: 2080 helix: 1.98 (0.17), residues: 1096 sheet: 0.81 (0.31), residues: 312 loop : -0.04 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.14 (10332) covalent geometry : angle 0.38364 / 0.25 (14340) hydrogen bonds : bond 0.02503 / 1.91 ( 814) hydrogen bonds : angle 4.39653 / 3.37 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0067 time to fit residues: 0.1388 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.038 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0068 time to fit residues: 0.1255 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 198 optimal weight: 0.0670 chunk 162 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 156 optimal weight: 50.0000 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 overall best weight: 5.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085327 restraints weight = 8663.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085327 restraints weight = 8681.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085327 restraints weight = 8681.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085327 restraints weight = 8681.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085327 restraints weight = 8681.300| |-----------------------------------------------------------------------------| r_work (final): 0.3150 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.054115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.045207 restraints weight = 8229.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.046003 restraints weight = 6320.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.046615 restraints weight = 5118.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.047060 restraints weight = 4305.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.047506 restraints weight = 3766.467| |-----------------------------------------------------------------------------| r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 1.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 10332 Z= 0.211 Angle : 0.432 2.748 14340 Z= 0.294 Chirality : 0.046 0.120 1928 Planarity : 0.002 0.014 2092 Dihedral : 3.662 11.231 2092 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 2080 helix: 1.54 (0.16), residues: 1092 sheet: 0.13 (0.28), residues: 352 loop : -0.19 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.21 (10332) covalent geometry : angle 0.43153 / 0.29 (14340) hydrogen bonds : bond 0.03139 / 2.41 ( 814) hydrogen bonds : angle 4.97700 / 3.81 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0083 time to fit residues: 0.1548 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.056 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.042 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0063 time to fit residues: 0.0990 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 85 optimal weight: 20.0000 chunk 100 optimal weight: 0.4980 chunk 152 optimal weight: 40.0000 chunk 178 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 128 optimal weight: 0.0980 chunk 87 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.089945 restraints weight = 7190.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090361 restraints weight = 6608.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.090830 restraints weight = 6184.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091264 restraints weight = 5834.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091379 restraints weight = 5578.210| |-----------------------------------------------------------------------------| r_work (final): 0.3227 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.054642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.045245 restraints weight = 7738.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.046068 restraints weight = 5912.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.046806 restraints weight = 4796.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.047381 restraints weight = 3976.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.047726 restraints weight = 3426.840| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 1.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 10332 Z= 0.155 Angle : 0.391 2.711 14340 Z= 0.261 Chirality : 0.046 0.130 1928 Planarity : 0.002 0.013 2092 Dihedral : 3.355 10.463 2092 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2080 helix: 1.98 (0.16), residues: 1096 sheet: 0.23 (0.29), residues: 336 loop : -0.49 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.16 (10332) covalent geometry : angle 0.39058 / 0.26 (14340) hydrogen bonds : bond 0.02603 / 1.99 ( 814) hydrogen bonds : angle 4.55595 / 3.49 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.068 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0094 time to fit residues: 0.1816 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.066 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.051 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0067 time to fit residues: 0.1202 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 88 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 81 optimal weight: 0.0060 chunk 52 optimal weight: 40.0000 overall best weight: 4.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085409 restraints weight = 8795.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085409 restraints weight = 8757.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085409 restraints weight = 8757.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085409 restraints weight = 8757.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085409 restraints weight = 8757.956| |-----------------------------------------------------------------------------| r_work (final): 0.3147 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.054393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.045575 restraints weight = 7845.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.046406 restraints weight = 6031.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.046986 restraints weight = 4854.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.047557 restraints weight = 4098.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.047926 restraints weight = 3515.270| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 1.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 10332 Z= 0.174 Angle : 0.402 2.701 14340 Z= 0.271 Chirality : 0.046 0.127 1928 Planarity : 0.002 0.013 2092 Dihedral : 3.448 10.629 2092 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 2080 helix: 2.11 (0.16), residues: 1072 sheet: 0.36 (0.28), residues: 340 loop : -0.52 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.17 (10332) covalent geometry : angle 0.40199 / 0.27 (14340) hydrogen bonds : bond 0.02800 / 2.15 ( 814) hydrogen bonds : angle 4.68622 / 3.59 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 888.81 seconds wall clock time: 15 minutes 53.53 seconds (953.53 seconds total)