Starting phenix.real_space_refine on Sat Aug 23 06:25:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uxa_20931/08_2025/6uxa_20931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uxa_20931/08_2025/6uxa_20931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uxa_20931/08_2025/6uxa_20931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uxa_20931/08_2025/6uxa_20931.map" model { file = "/net/cci-nas-00/data/ceres_data/6uxa_20931/08_2025/6uxa_20931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uxa_20931/08_2025/6uxa_20931.cif" } resolution = 4.5 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-2.0-5787/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: 2.47, per 1000 atoms: 0.24 Number of scatterers: 10344 At special positions: 0 Unit cell: (138.03, 138.03, 120.91, 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: 1.13 Conformation dependent library (CDL) restraints added in 573.2 milliseconds Enol-peptide restraints added in 715.3 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: 0.48 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: 3.692A 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: 3.535A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.502A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.832A 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: 3.649A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.586A 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: 3.749A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 3.563A pdb=" N ASP E 284 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 334 Processing helix chain '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: 4.892A pdb=" N GLY C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.278A 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: 3.807A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.535A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.502A 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: 3.813A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.705A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.647A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.588A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.590A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.548A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.563A 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: 4.277A pdb=" N THR B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.564A 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: 3.791A pdb=" N ALA B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.693A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.530A 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: 3.941A 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: 3.583A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 241 removed outlier: 3.564A 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: 3.599A 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: 4.894A pdb=" N GLY D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.692A 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: 3.790A pdb=" N ALA D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.694A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.531A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 148 through 154 Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.941A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.708A 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: 3.788A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.599A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.582A 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: 7.172A 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: 5.685A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.499A pdb=" N VAL E 139 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL E 160 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 141 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.570A 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: 7.175A 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: 6.720A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.498A pdb=" N VAL G 139 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL G 160 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL G 141 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.060A 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: 6.907A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.493A 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: 7.457A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.865A 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: 7.734A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N HIS B 117 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 180 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 208 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.096A 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: 7.908A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 209 " --> pdb=" O ILE B 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 268 removed outlier: 7.239A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.392A 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: 5.840A 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: 7.229A 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: 6.548A 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: 5.866A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS D 117 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 180 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE D 208 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 7.908A 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) 813 hydrogen bonds defined for protein. 2355 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: 1.81 Time building geometry restraints manager: 1.41 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: 2112 1.51 - 1.58: 4024 Bond restraints: 10332 Sorted by residual: 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 7.88e+00 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 7.79e+00 bond pdb=" CA VAL A 55 " pdb=" CB VAL A 55 " ideal model delta sigma weight residual 1.542 1.579 -0.038 1.45e-02 4.76e+03 6.80e+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 6.53e+00 bond pdb=" CA VAL B 55 " pdb=" CB VAL B 55 " ideal model delta sigma weight residual 1.542 1.578 -0.037 1.45e-02 4.76e+03 6.39e+00 ... (remaining 10327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 11879 0.93 - 1.86: 2003 1.86 - 2.79: 332 2.79 - 3.72: 97 3.72 - 4.65: 29 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 119.76 116.53 3.23 1.00e+00 1.00e+00 1.04e+01 angle pdb=" C SER B 66 " pdb=" N PRO B 67 " pdb=" CA PRO B 67 " ideal model delta sigma weight residual 119.76 116.57 3.19 1.00e+00 1.00e+00 1.02e+01 angle pdb=" C SER C 66 " pdb=" N PRO C 67 " pdb=" CA PRO C 67 " ideal model delta sigma weight residual 119.76 116.63 3.13 1.00e+00 1.00e+00 9.77e+00 angle pdb=" N GLU D 171 " pdb=" CA GLU D 171 " pdb=" C GLU D 171 " ideal model delta sigma weight residual 111.28 114.63 -3.35 1.09e+00 8.42e-01 9.45e+00 angle pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 111.28 114.63 -3.35 1.09e+00 8.42e-01 9.44e+00 ... (remaining 14335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.04: 4804 3.04 - 6.08: 765 6.08 - 9.11: 256 9.11 - 12.15: 95 12.15 - 15.19: 28 Dihedral angle restraints: 5948 sinusoidal: 0 harmonic: 5948 Sorted by residual: dihedral pdb=" C VAL A 27 " pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta harmonic sigma weight residual -122.00 -131.25 9.25 0 2.50e+00 1.60e-01 1.37e+01 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 -131.22 9.22 0 2.50e+00 1.60e-01 1.36e+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 -131.20 9.20 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 5945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1372 0.060 - 0.119: 430 0.119 - 0.179: 112 0.179 - 0.239: 10 0.239 - 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 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 2.23 0.29 2.00e-01 2.50e+01 2.14e+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 2.23 0.29 2.00e-01 2.50e+01 2.12e+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 2.93e-02 8.58e+00 pdb=" C ASP B 169 " -0.051 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 8.33e+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 1.93e-02 3.74e+00 pdb=" C VAL B 267 " -0.033 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: 6551 3.09 - 3.54: 10954 3.54 - 4.00: 12158 4.00 - 4.45: 13949 4.45 - 4.90: 22647 Nonbonded interactions: 66259 Sorted by model distance: nonbonded pdb=" N GLY G 136 " pdb=" N SER G 137 " model vdw 2.638 2.560 nonbonded pdb=" N GLY E 136 " pdb=" N SER E 137 " model vdw 2.638 2.560 nonbonded pdb=" N SER B 66 " pdb=" O SER B 66 " model vdw 2.640 2.496 nonbonded pdb=" N SER D 66 " pdb=" O SER D 66 " model vdw 2.640 2.496 nonbonded pdb=" N VAL D 181 " pdb=" O ARG D 206 " model vdw 2.640 3.120 ... (remaining 66254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.400 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 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 4.654 14340 Z= 0.537 Chirality : 0.063 0.298 1928 Planarity : 0.004 0.029 2092 Dihedral : 4.562 15.189 2092 Min Nonbonded Distance : 2.638 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 0.00460 (10332) covalent geometry : angle 0.77458 (14340) hydrogen bonds : bond 0.16821 ( 813) hydrogen bonds : angle 6.98591 ( 2355) *********************** 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 : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0101 time to fit residues: 0.1516 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 : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0067 time to fit residues: 0.1079 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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.0020 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 11.9990 chunk 122 optimal weight: 10.9990 overall best weight: 5.7996 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.164419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133326 restraints weight = 7177.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.135188 restraints weight = 5879.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136745 restraints weight = 4960.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.138049 restraints weight = 4285.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.139144 restraints weight = 3764.042| |-----------------------------------------------------------------------------| r_work (final): 0.3839 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.068317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.057676 restraints weight = 6725.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.058690 restraints weight = 5148.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.059375 restraints weight = 4138.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.060114 restraints weight = 3482.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.060655 restraints weight = 2990.002| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 1.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10332 Z= 0.268 Angle : 0.635 7.373 14340 Z= 0.419 Chirality : 0.048 0.141 1928 Planarity : 0.004 0.032 2092 Dihedral : 4.881 24.031 2092 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.12 % 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: -0.24 (0.17), residues: 2080 helix: 0.16 (0.15), residues: 1076 sheet: 1.08 (0.25), residues: 336 loop : -1.20 (0.21), 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 0.00361 (10332) covalent geometry : angle 0.63512 (14340) hydrogen bonds : bond 0.04875 ( 813) hydrogen bonds : angle 5.25909 ( 2355) *********************** 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 : 0.051 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0081 time to fit residues: 0.1528 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 : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0043 time to fit residues: 0.0651 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 16 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 111 optimal weight: 50.0000 chunk 81 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 overall best weight: 3.2584 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.171177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.137901 restraints weight = 6682.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.139565 restraints weight = 5632.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140816 restraints weight = 4875.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.142231 restraints weight = 4311.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.143163 restraints weight = 3834.908| |-----------------------------------------------------------------------------| r_work (final): 0.3888 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.052350 restraints weight = 6080.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.053341 restraints weight = 4757.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.054100 restraints weight = 3935.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.054845 restraints weight = 3368.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.055354 restraints weight = 2928.798| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 1.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10332 Z= 0.162 Angle : 0.475 6.133 14340 Z= 0.309 Chirality : 0.048 0.136 1928 Planarity : 0.004 0.031 2092 Dihedral : 3.894 17.756 2092 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.46 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 : 0.00 % 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: 1.04 (0.18), residues: 2080 helix: 1.51 (0.17), residues: 1068 sheet: 1.27 (0.30), residues: 280 loop : -0.74 (0.20), residues: 732 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 0.00219 (10332) covalent geometry : angle 0.47533 (14340) hydrogen bonds : bond 0.02980 ( 813) hydrogen bonds : angle 4.51331 ( 2355) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 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 : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0122 time to fit residues: 0.1519 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 : 0.060 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0065 time to fit residues: 0.1031 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 51 optimal weight: 0.0980 chunk 131 optimal weight: 20.0000 chunk 207 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 62 optimal weight: 0.0670 chunk 173 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 chunk 126 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.2638 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.173214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141142 restraints weight = 6600.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142979 restraints weight = 5492.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.144186 restraints weight = 4701.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145644 restraints weight = 4145.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.146700 restraints weight = 3683.596| |-----------------------------------------------------------------------------| r_work (final): 0.4082 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.065525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.053369 restraints weight = 5970.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.054366 restraints weight = 4655.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.055199 restraints weight = 3832.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.055887 restraints weight = 3271.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.056383 restraints weight = 2860.554| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 1.6222 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= 0.092 Angle : 0.388 6.410 14340 Z= 0.244 Chirality : 0.048 0.130 1928 Planarity : 0.003 0.024 2092 Dihedral : 3.375 17.340 2092 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.13 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: 1.40 (0.19), residues: 2080 helix: 1.87 (0.17), residues: 1068 sheet: 0.57 (0.29), residues: 312 loop : -0.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 33 PHE 0.000 0.000 PHE A 38 TRP 0.000 0.000 TRP A 46 Details of bonding type rmsd covalent geometry : bond 0.00122 (10332) covalent geometry : angle 0.38766 (14340) hydrogen bonds : bond 0.01979 ( 813) hydrogen bonds : angle 3.91805 ( 2355) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 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 : 0.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0083 time to fit residues: 0.1639 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 : 0.061 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0070 time to fit residues: 0.1182 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 : 0.037 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 8.9990 chunk 4 optimal weight: 0.0970 chunk 168 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 chunk 50 optimal weight: 0.8980 overall best weight: 1.6780 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.174620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.141603 restraints weight = 6567.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.143177 restraints weight = 5594.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.144568 restraints weight = 4881.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145480 restraints weight = 4318.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.146605 restraints weight = 3908.974| |-----------------------------------------------------------------------------| r_work (final): 0.3949 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.063593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.051931 restraints weight = 6242.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.052942 restraints weight = 4918.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.053770 restraints weight = 4044.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.054408 restraints weight = 3448.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.054828 restraints weight = 3014.959| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 1.6372 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= 0.105 Angle : 0.395 5.395 14340 Z= 0.253 Chirality : 0.047 0.131 1928 Planarity : 0.003 0.025 2092 Dihedral : 3.428 19.877 2092 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 1.94 (0.19), residues: 2080 helix: 2.29 (0.17), residues: 1072 sheet: 0.97 (0.30), residues: 280 loop : -0.06 (0.23), residues: 728 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 0.00141 (10332) covalent geometry : angle 0.39459 (14340) hydrogen bonds : bond 0.02103 ( 813) hydrogen bonds : angle 3.82395 ( 2355) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 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 : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0052 time to fit residues: 0.0937 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: 0.0076 time to fit residues: 0.1093 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 8 optimal weight: 0.0020 chunk 192 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 146 optimal weight: 0.0010 overall best weight: 3.8000 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.181408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.147926 restraints weight = 6321.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.149621 restraints weight = 5339.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.151156 restraints weight = 4616.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.152129 restraints weight = 4067.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.153357 restraints weight = 3651.656| |-----------------------------------------------------------------------------| r_work (final): 0.4040 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.059860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.048666 restraints weight = 6596.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.049599 restraints weight = 5241.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.050192 restraints weight = 4337.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.050953 restraints weight = 3759.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.051381 restraints weight = 3270.107| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 1.6698 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= 0.164 Angle : 0.473 5.954 14340 Z= 0.305 Chirality : 0.046 0.125 1928 Planarity : 0.003 0.019 2092 Dihedral : 4.373 21.122 2092 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: 1.04 (0.19), residues: 2080 helix: 1.61 (0.16), residues: 1068 sheet: 0.28 (0.31), residues: 276 loop : -0.44 (0.23), residues: 736 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 0.00220 (10332) covalent geometry : angle 0.47319 (14340) hydrogen bonds : bond 0.02999 ( 813) hydrogen bonds : angle 4.85342 ( 2355) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 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: 0.0080 time to fit residues: 0.1487 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.051 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0065 time to fit residues: 0.1012 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 143 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 201 optimal weight: 0.0170 chunk 104 optimal weight: 60.0000 chunk 72 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 overall best weight: 7.0026 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.153224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117644 restraints weight = 8295.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118250 restraints weight = 7185.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118936 restraints weight = 6297.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118936 restraints weight = 5603.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118936 restraints weight = 5603.922| |-----------------------------------------------------------------------------| r_work (final): 0.3636 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.058014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.047252 restraints weight = 6830.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.048204 restraints weight = 5371.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.048948 restraints weight = 4419.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.049612 restraints weight = 3749.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.050072 restraints weight = 3246.264| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 1.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 10332 Z= 0.271 Angle : 0.564 4.676 14340 Z= 0.378 Chirality : 0.046 0.128 1928 Planarity : 0.004 0.024 2092 Dihedral : 5.093 29.410 2092 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.73 % 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: -0.44 (0.18), residues: 2080 helix: 0.42 (0.16), residues: 1052 sheet: -1.03 (0.29), residues: 280 loop : -0.85 (0.23), residues: 748 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 0.00364 (10332) covalent geometry : angle 0.56421 (14340) hydrogen bonds : bond 0.04092 ( 813) hydrogen bonds : angle 5.73232 ( 2355) *********************** 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 : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0074 time to fit residues: 0.1358 Evaluate side-chains 5 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.053 Evaluate side-chains 4 residues out of total 190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0066 time to fit residues: 0.1029 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3085 > 50: distance: 0 - 17: 47.215 distance: 2 - 3: 22.162 distance: 3 - 4: 21.132 distance: 3 - 6: 30.418 distance: 4 - 5: 56.054 distance: 4 - 7: 11.975 distance: 7 - 8: 14.516 distance: 8 - 9: 47.910 distance: 8 - 11: 57.735 distance: 9 - 10: 40.116 distance: 9 - 12: 39.490 distance: 13 - 16: 61.290 distance: 14 - 15: 47.945 distance: 14 - 17: 56.822 distance: 17 - 18: 55.509 distance: 18 - 19: 40.492 distance: 19 - 20: 48.225 distance: 21 - 22: 57.150 distance: 22 - 23: 50.690 distance: 22 - 25: 39.607 distance: 23 - 24: 50.243 distance: 23 - 26: 41.254 distance: 26 - 27: 45.896 distance: 27 - 28: 46.769 distance: 27 - 30: 17.023 distance: 28 - 29: 40.385 distance: 28 - 31: 69.206 distance: 33 - 34: 40.176 distance: 33 - 36: 35.429 distance: 36 - 37: 56.799 distance: 38 - 39: 56.052 distance: 38 - 41: 57.582 distance: 41 - 42: 48.755 distance: 42 - 43: 38.872 distance: 42 - 45: 56.750 distance: 43 - 44: 39.300 distance: 43 - 46: 56.767 distance: 46 - 47: 38.997 distance: 47 - 48: 57.145