Starting phenix.real_space_refine on Wed Sep 17 18:02:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uxb_20932/09_2025/6uxb_20932.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uxb_20932/09_2025/6uxb_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_20932/09_2025/6uxb_20932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uxb_20932/09_2025/6uxb_20932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uxb_20932/09_2025/6uxb_20932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uxb_20932/09_2025/6uxb_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-2.0-5805/lib/python3.9/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: 2.97, per 1000 atoms: 0.29 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: 1.08 Conformation dependent library (CDL) restraints added in 714.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.53 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: 1.84 Time building geometry restraints manager: 1.37 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: 0.950 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.030 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 aren 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 covalent geometry : bond 0.00459 (10332) covalent geometry : angle 0.77489 (14340) hydrogen bonds : bond 0.16820 ( 814) hydrogen bonds : angle 6.99762 ( 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 : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0091 time to fit residues: 0.1184 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 : 0.054 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0067 time to fit residues: 0.1059 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=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... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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: 0.7074 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 aren 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 covalent geometry : bond 0.00471 (10332) covalent geometry : angle 0.68454 (14340) hydrogen bonds : bond 0.05208 ( 814) hydrogen bonds : angle 5.70618 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 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 : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0083 time to fit residues: 0.1483 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 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: 0.0044 time to fit residues: 0.0910 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: 8.9990 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: 4.9990 chunk 29 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 overall best weight: 3.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094505 restraints weight = 7455.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095075 restraints weight = 6895.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095725 restraints weight = 6460.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095725 restraints weight = 6107.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095725 restraints weight = 6107.147| |-----------------------------------------------------------------------------| r_work (final): 0.3319 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.059957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.050209 restraints weight = 7487.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.051042 restraints weight = 5912.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.051707 restraints weight = 4851.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.052319 restraints weight = 4133.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.052757 restraints weight = 3612.455| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 1.0924 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= 0.144 Angle : 0.427 3.976 14340 Z= 0.279 Chirality : 0.048 0.132 1928 Planarity : 0.003 0.032 2092 Dihedral : 3.782 15.078 2092 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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 aren not related in a simple way. whole: 0.86 (0.18), residues: 2080 helix: 1.10 (0.16), residues: 1076 sheet: 0.88 (0.29), residues: 316 loop : -0.28 (0.21), residues: 688 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 covalent geometry : bond 0.00193 (10332) covalent geometry : angle 0.42742 (14340) hydrogen bonds : bond 0.02774 ( 814) hydrogen bonds : angle 4.40470 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 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: 0.0095 time to fit residues: 0.1858 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 : 0.070 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 : 0.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0070 time to fit residues: 0.1191 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 : 0.064 ------------------------------------------------------------------------------- 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: 9.9990 chunk 131 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 152 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 173 optimal weight: 30.0000 chunk 8 optimal weight: 0.0670 chunk 106 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 overall best weight: 7.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.121522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100809 restraints weight = 7393.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101464 restraints weight = 6851.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101851 restraints weight = 6402.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102507 restraints weight = 6089.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102784 restraints weight = 5756.941| |-----------------------------------------------------------------------------| r_work (final): 0.3472 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.054132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.045719 restraints weight = 8301.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.046466 restraints weight = 6447.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.047146 restraints weight = 5271.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.047486 restraints weight = 4423.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.047962 restraints weight = 3930.639| |-----------------------------------------------------------------------------| r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 1.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 10332 Z= 0.333 Angle : 0.606 4.947 14340 Z= 0.415 Chirality : 0.046 0.128 1928 Planarity : 0.005 0.032 2092 Dihedral : 5.149 17.988 2092 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.11 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 aren not related in a simple way. whole: -0.57 (0.18), residues: 2080 helix: -0.41 (0.14), residues: 1084 sheet: 0.08 (0.30), residues: 328 loop : -0.19 (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 covalent geometry : bond 0.00445 (10332) covalent geometry : angle 0.60618 (14340) hydrogen bonds : bond 0.04766 ( 814) hydrogen bonds : angle 6.06510 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 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 : 0.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0081 time to fit residues: 0.1500 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 : 0.032 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 : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0043 time to fit residues: 0.0649 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 : 0.024 ------------------------------------------------------------------------------- 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: 10.0000 chunk 157 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 29 optimal weight: 0.0980 chunk 151 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103115 restraints weight = 7152.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103856 restraints weight = 6663.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.104219 restraints weight = 6238.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.104800 restraints weight = 5946.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105344 restraints weight = 5640.668| |-----------------------------------------------------------------------------| r_work (final): 0.3509 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.056503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.047069 restraints weight = 7759.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.047950 restraints weight = 6016.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.048746 restraints weight = 4874.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.049319 restraints weight = 4062.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.049814 restraints weight = 3499.537| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 1.1699 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= 0.154 Angle : 0.421 4.095 14340 Z= 0.279 Chirality : 0.047 0.125 1928 Planarity : 0.003 0.027 2092 Dihedral : 4.023 15.500 2092 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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 aren not related in a simple way. whole: 0.58 (0.19), residues: 2080 helix: 0.78 (0.16), residues: 1076 sheet: 0.24 (0.32), residues: 316 loop : 0.05 (0.24), residues: 688 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 covalent geometry : bond 0.00206 (10332) covalent geometry : angle 0.42146 (14340) hydrogen bonds : bond 0.02867 ( 814) hydrogen bonds : angle 4.78407 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 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 : 0.053 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0087 time to fit residues: 0.1618 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 : 0.045 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0081 time to fit residues: 0.1153 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 146 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.110155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088117 restraints weight = 8820.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088117 restraints weight = 8836.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088117 restraints weight = 8836.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088117 restraints weight = 8836.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088117 restraints weight = 8836.695| |-----------------------------------------------------------------------------| r_work (final): 0.3225 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.051715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.042252 restraints weight = 7880.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.043013 restraints weight = 6206.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.043560 restraints weight = 5117.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.044002 restraints weight = 4400.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.044369 restraints weight = 3897.719| |-----------------------------------------------------------------------------| r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 1.2113 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= 0.245 Angle : 0.501 4.839 14340 Z= 0.339 Chirality : 0.047 0.140 1928 Planarity : 0.004 0.027 2092 Dihedral : 4.595 15.560 2092 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % 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 aren not related in a simple way. whole: -0.04 (0.18), residues: 2080 helix: 0.28 (0.16), residues: 1064 sheet: -0.11 (0.30), residues: 324 loop : -0.20 (0.24), 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 covalent geometry : bond 0.00327 (10332) covalent geometry : angle 0.50128 (14340) hydrogen bonds : bond 0.03773 ( 814) hydrogen bonds : angle 5.53306 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 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 : 0.055 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0083 time to fit residues: 0.1540 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 : 0.057 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0065 time to fit residues: 0.1045 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 : 0.048 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 104 optimal weight: 50.0000 chunk 72 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 26 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 overall best weight: 4.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.084393 restraints weight = 7855.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084502 restraints weight = 7505.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084502 restraints weight = 7264.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084502 restraints weight = 7264.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084502 restraints weight = 7264.441| |-----------------------------------------------------------------------------| r_work (final): 0.3237 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.052493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.042937 restraints weight = 7592.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.043742 restraints weight = 5878.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.044307 restraints weight = 4835.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.044773 restraints weight = 4151.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.045146 restraints weight = 3653.049| |-----------------------------------------------------------------------------| r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 1.2093 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= 0.181 Angle : 0.435 4.707 14340 Z= 0.291 Chirality : 0.047 0.131 1928 Planarity : 0.003 0.025 2092 Dihedral : 4.031 16.138 2092 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % 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 aren not related in a simple way. whole: -0.01 (0.19), residues: 2080 helix: 0.52 (0.16), residues: 1088 sheet: -0.51 (0.30), residues: 328 loop : -0.35 (0.25), 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 covalent geometry : bond 0.00243 (10332) covalent geometry : angle 0.43528 (14340) hydrogen bonds : bond 0.02845 ( 814) hydrogen bonds : angle 4.93877 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 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 : 0.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0080 time to fit residues: 0.1513 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 : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0065 time to fit residues: 0.1026 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=2.00 ------------------------------------------------------------------------------- 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: 7.9990 chunk 7 optimal weight: 40.0000 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 138 optimal weight: 0.0020 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089022 restraints weight = 8868.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089022 restraints weight = 8775.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089022 restraints weight = 8775.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089022 restraints weight = 8775.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089022 restraints weight = 8775.580| |-----------------------------------------------------------------------------| r_work (final): 0.3268 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.052575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.042890 restraints weight = 7388.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.043534 restraints weight = 5752.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.044176 restraints weight = 4798.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.044653 restraints weight = 4147.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.044961 restraints weight = 3672.823| |-----------------------------------------------------------------------------| r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 1.2125 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= 0.134 Angle : 0.400 3.857 14340 Z= 0.265 Chirality : 0.047 0.129 1928 Planarity : 0.003 0.022 2092 Dihedral : 3.725 16.342 2092 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % 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 aren not related in a simple way. whole: 0.37 (0.19), residues: 2080 helix: 0.99 (0.16), residues: 1088 sheet: -0.65 (0.29), residues: 324 loop : -0.32 (0.26), 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 covalent geometry : bond 0.00179 (10332) covalent geometry : angle 0.40033 (14340) hydrogen bonds : bond 0.02397 ( 814) hydrogen bonds : angle 4.52260 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 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 : 0.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0081 time to fit residues: 0.1492 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 : 0.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0067 time to fit residues: 0.1078 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 198 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 33 optimal weight: 0.4980 chunk 183 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 132 optimal weight: 0.4980 chunk 144 optimal weight: 0.0670 chunk 69 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.112921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090644 restraints weight = 8816.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090644 restraints weight = 8615.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090644 restraints weight = 8618.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090644 restraints weight = 8618.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090644 restraints weight = 8618.616| |-----------------------------------------------------------------------------| r_work (final): 0.3292 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.054068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.044020 restraints weight = 7220.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.044827 restraints weight = 5593.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.045421 restraints weight = 4624.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.046000 restraints weight = 3897.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.046348 restraints weight = 3456.724| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 1.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.007 10332 Z= 0.080 Angle : 0.367 3.478 14340 Z= 0.237 Chirality : 0.047 0.128 1928 Planarity : 0.003 0.021 2092 Dihedral : 3.448 16.512 2092 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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 aren not related in a simple way. whole: 0.97 (0.20), residues: 2080 helix: 1.57 (0.17), residues: 1092 sheet: -0.30 (0.31), residues: 308 loop : -0.29 (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 covalent geometry : bond 0.00107 (10332) covalent geometry : angle 0.36726 (14340) hydrogen bonds : bond 0.01860 ( 814) hydrogen bonds : angle 4.03714 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 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: 0.0082 time to fit residues: 0.1563 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 : 0.057 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: 0.0056 time to fit residues: 0.0875 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 85 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 152 optimal weight: 0.0770 chunk 178 optimal weight: 10.0000 chunk 151 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 128 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 overall best weight: 4.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087557 restraints weight = 9015.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087557 restraints weight = 8881.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087557 restraints weight = 8881.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087557 restraints weight = 8881.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087557 restraints weight = 8881.754| |-----------------------------------------------------------------------------| r_work (final): 0.3186 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.052190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.042400 restraints weight = 7599.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.043037 restraints weight = 5917.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.043691 restraints weight = 4947.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.044200 restraints weight = 4247.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.044495 restraints weight = 3735.408| |-----------------------------------------------------------------------------| r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 1.2248 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= 0.187 Angle : 0.426 3.555 14340 Z= 0.287 Chirality : 0.046 0.127 1928 Planarity : 0.003 0.022 2092 Dihedral : 3.717 17.058 2092 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % 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 aren not related in a simple way. whole: 0.42 (0.19), residues: 2080 helix: 1.07 (0.16), residues: 1092 sheet: -0.76 (0.30), residues: 324 loop : -0.30 (0.25), 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 covalent geometry : bond 0.00250 (10332) covalent geometry : angle 0.42556 (14340) hydrogen bonds : bond 0.02659 ( 814) hydrogen bonds : angle 4.64655 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 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 : 0.053 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0080 time to fit residues: 0.1501 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 : 0.054 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0065 time to fit residues: 0.1043 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 88 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 48 optimal weight: 0.0060 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 52 optimal weight: 40.0000 overall best weight: 2.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088260 restraints weight = 9137.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088261 restraints weight = 9003.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088261 restraints weight = 9000.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088261 restraints weight = 9000.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088261 restraints weight = 9000.349| |-----------------------------------------------------------------------------| r_work (final): 0.3257 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.052888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.043004 restraints weight = 7312.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.043649 restraints weight = 5668.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.044349 restraints weight = 4710.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.044835 restraints weight = 4047.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.045186 restraints weight = 3566.247| |-----------------------------------------------------------------------------| r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 1.2236 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= 0.123 Angle : 0.386 3.456 14340 Z= 0.254 Chirality : 0.047 0.127 1928 Planarity : 0.003 0.021 2092 Dihedral : 3.542 16.984 2092 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % 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 aren not related in a simple way. whole: 0.61 (0.20), residues: 2080 helix: 1.32 (0.17), residues: 1092 sheet: -0.86 (0.29), residues: 348 loop : -0.26 (0.26), residues: 640 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 covalent geometry : bond 0.00164 (10332) covalent geometry : angle 0.38556 (14340) hydrogen bonds : bond 0.02195 ( 814) hydrogen bonds : angle 4.33487 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 952.41 seconds wall clock time: 17 minutes 19.55 seconds (1039.55 seconds total)