Starting phenix.real_space_refine on Mon Jun 16 09:57:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6olk_20115/06_2025/6olk_20115.cif Found real_map, /net/cci-nas-00/data/ceres_data/6olk_20115/06_2025/6olk_20115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6olk_20115/06_2025/6olk_20115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6olk_20115/06_2025/6olk_20115.map" model { file = "/net/cci-nas-00/data/ceres_data/6olk_20115/06_2025/6olk_20115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6olk_20115/06_2025/6olk_20115.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10281 atoms to isotropic. 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 6138 2.51 5 N 2094 2.21 5 O 2091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10323 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 1720 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 328} Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1061 Unresolved non-hydrogen angles: 1356 Unresolved non-hydrogen dihedrals: 850 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "B" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 1721 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 328} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1057 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 848 Unresolved non-hydrogen chiralities: 115 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 1720 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 328} Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1061 Unresolved non-hydrogen angles: 1356 Unresolved non-hydrogen dihedrals: 850 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 1721 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 328} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1057 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 848 Unresolved non-hydrogen chiralities: 115 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 1720 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 328} Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1061 Unresolved non-hydrogen angles: 1356 Unresolved non-hydrogen dihedrals: 850 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "F" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 1721 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 328} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1057 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 848 Unresolved non-hydrogen chiralities: 115 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Time building chain proxies: 6.67, per 1000 atoms: 0.65 Number of scatterers: 10323 At special positions: 0 Unit cell: (122.96, 126.14, 78.44, 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 2091 8.00 N 2094 7.00 C 6138 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: 2.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 48.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 113 through 120 removed outlier: 4.341A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 288 through 297 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 113 through 120 removed outlier: 3.891A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 288 through 297 Processing helix chain 'B' and resid 301 through 310 removed outlier: 4.119A pdb=" N SER B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 343 through 350 Processing helix chain 'C' and resid 4 through 14 Processing helix chain 'C' and resid 44 through 55 removed outlier: 3.735A pdb=" N ILE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 Processing helix chain 'C' and resid 114 through 120 Processing helix chain 'C' and resid 136 through 152 Processing helix chain 'C' and resid 185 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 302 through 309 Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 333 through 341 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'D' and resid 3 through 14 Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 57 through 68 Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 113 through 120 removed outlier: 3.973A pdb=" N ARG D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 Processing helix chain 'D' and resid 185 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 249 through 260 removed outlier: 3.505A pdb=" N VAL D 253 " --> pdb=" O GLN D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 301 through 310 removed outlier: 4.301A pdb=" N SER D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 333 through 339 removed outlier: 3.523A pdb=" N GLY D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 350 Processing helix chain 'E' and resid 4 through 14 Processing helix chain 'E' and resid 44 through 54 Processing helix chain 'E' and resid 57 through 68 Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 113 through 120 removed outlier: 4.351A pdb=" N ARG E 117 " --> pdb=" O PRO E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 233 through 244 removed outlier: 3.530A pdb=" N VAL E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 288 through 297 Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 302 through 309 Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 318 through 329 Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'F' and resid 3 through 14 Processing helix chain 'F' and resid 44 through 54 Processing helix chain 'F' and resid 57 through 68 Processing helix chain 'F' and resid 106 through 111 Processing helix chain 'F' and resid 113 through 120 removed outlier: 3.937A pdb=" N ARG F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 208 through 221 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 249 through 260 Processing helix chain 'F' and resid 288 through 297 Processing helix chain 'F' and resid 301 through 310 removed outlier: 4.303A pdb=" N SER F 305 " --> pdb=" O HIS F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 315 Processing helix chain 'F' and resid 318 through 329 Processing helix chain 'F' and resid 333 through 339 Processing helix chain 'F' and resid 343 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 4.007A pdb=" N ASP A 18 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 178 removed outlier: 6.657A pdb=" N ILE A 156 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ARG A 177 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR A 158 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS A 155 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU A 202 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 157 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLY A 204 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL A 159 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 203 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR A 228 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU A 205 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS A 225 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 127 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 227 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU A 126 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 263 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.782A pdb=" N GLN B 28 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 30 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP B 18 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 81 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 178 removed outlier: 6.699A pdb=" N ILE B 156 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG B 177 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 158 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS B 155 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU B 202 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 157 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLY B 204 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N VAL B 159 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 201 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR B 228 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL B 203 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY B 125 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 227 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 127 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU B 229 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 129 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 126 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 263 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.000A pdb=" N ASP C 18 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 173 through 178 removed outlier: 6.666A pdb=" N ILE C 156 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ARG C 177 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 158 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N HIS C 155 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU C 202 " --> pdb=" O HIS C 155 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C 157 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLY C 204 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N VAL C 159 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 203 " --> pdb=" O PHE C 226 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR C 228 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLU C 205 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS C 225 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 127 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU C 126 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 263 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.811A pdb=" N GLN D 28 " --> pdb=" O HIS D 20 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 30 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP D 18 " --> pdb=" O ARG D 30 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG D 81 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 178 removed outlier: 6.729A pdb=" N ILE D 156 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ARG D 177 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR D 158 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY D 204 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 201 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR D 228 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N VAL D 203 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY D 125 " --> pdb=" O CYS D 225 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA D 227 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 127 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU D 229 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL D 129 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU D 126 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 263 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 37 removed outlier: 4.127A pdb=" N ASP E 18 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.693A pdb=" N ILE E 156 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ARG E 177 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 158 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N HIS E 155 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU E 202 " --> pdb=" O HIS E 155 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E 157 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLY E 204 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL E 159 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 203 " --> pdb=" O PHE E 226 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR E 228 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU E 205 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS E 225 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 127 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU E 126 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU E 265 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU E 128 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN E 267 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR E 130 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU E 269 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 34 through 37 removed outlier: 3.780A pdb=" N GLN F 28 " --> pdb=" O HIS F 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG F 30 " --> pdb=" O ASP F 18 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP F 18 " --> pdb=" O ARG F 30 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG F 81 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 173 through 178 removed outlier: 6.719A pdb=" N ILE F 156 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ARG F 177 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR F 158 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY F 204 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL F 201 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR F 228 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N VAL F 203 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY F 125 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA F 227 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL F 127 " --> pdb=" O ALA F 227 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU F 229 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL F 129 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU F 126 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 263 " --> pdb=" O LEU F 126 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2451 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2091 1.29 - 1.35: 2086 1.35 - 1.42: 2 1.42 - 1.48: 2094 1.48 - 1.55: 4044 Bond restraints: 10317 Sorted by residual: bond pdb=" C ASP A 197 " pdb=" O ASP A 197 " ideal model delta sigma weight residual 1.233 1.243 -0.010 4.80e-03 4.34e+04 4.51e+00 bond pdb=" C ASP E 197 " pdb=" O ASP E 197 " ideal model delta sigma weight residual 1.233 1.223 0.010 4.80e-03 4.34e+04 4.49e+00 bond pdb=" CA PRO E 41 " pdb=" C PRO E 41 " ideal model delta sigma weight residual 1.517 1.528 -0.011 6.70e-03 2.23e+04 2.58e+00 bond pdb=" CA PHE E 226 " pdb=" CB PHE E 226 " ideal model delta sigma weight residual 1.532 1.505 0.026 1.74e-02 3.30e+03 2.31e+00 bond pdb=" N ILE A 100 " pdb=" CA ILE A 100 " ideal model delta sigma weight residual 1.456 1.469 -0.013 8.60e-03 1.35e+04 2.18e+00 ... (remaining 10312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12558 1.50 - 3.00: 1547 3.00 - 4.51: 192 4.51 - 6.01: 38 6.01 - 7.51: 11 Bond angle restraints: 14346 Sorted by residual: angle pdb=" C ILE F 100 " pdb=" CA ILE F 100 " pdb=" CB ILE F 100 " ideal model delta sigma weight residual 111.08 115.61 -4.53 9.50e-01 1.11e+00 2.27e+01 angle pdb=" N LEU C 224 " pdb=" CA LEU C 224 " pdb=" C LEU C 224 " ideal model delta sigma weight residual 108.41 115.83 -7.42 1.61e+00 3.86e-01 2.13e+01 angle pdb=" N LEU A 224 " pdb=" CA LEU A 224 " pdb=" C LEU A 224 " ideal model delta sigma weight residual 108.20 115.71 -7.51 1.71e+00 3.42e-01 1.93e+01 angle pdb=" N LEU B 202 " pdb=" CA LEU B 202 " pdb=" C LEU B 202 " ideal model delta sigma weight residual 108.52 101.52 7.00 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N LEU E 224 " pdb=" CA LEU E 224 " pdb=" C LEU E 224 " ideal model delta sigma weight residual 108.20 115.54 -7.34 1.71e+00 3.42e-01 1.84e+01 ... (remaining 14341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.56: 5044 3.56 - 7.12: 636 7.12 - 10.67: 191 10.67 - 14.23: 83 14.23 - 17.79: 34 Dihedral angle restraints: 5988 sinusoidal: 0 harmonic: 5988 Sorted by residual: dihedral pdb=" CA CYS C 172 " pdb=" C CYS C 172 " pdb=" N VAL C 173 " pdb=" CA VAL C 173 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU B 280 " pdb=" C LEU B 280 " pdb=" N ALA B 281 " pdb=" CA ALA B 281 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N ASN C 85 " pdb=" CA ASN C 85 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1221 0.045 - 0.090: 489 0.090 - 0.135: 183 0.135 - 0.180: 48 0.180 - 0.225: 9 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA VAL E 129 " pdb=" N VAL E 129 " pdb=" C VAL E 129 " pdb=" CB VAL E 129 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL C 129 " pdb=" N VAL C 129 " pdb=" C VAL C 129 " pdb=" CB VAL C 129 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL E 96 " pdb=" N VAL E 96 " pdb=" C VAL E 96 " pdb=" CB VAL E 96 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1947 not shown) Planarity restraints: 2085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 189 " 0.021 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C ALA B 189 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA B 189 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU B 190 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 189 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ALA F 189 " -0.068 2.00e-02 2.50e+03 pdb=" O ALA F 189 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU F 190 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 189 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ALA D 189 " 0.065 2.00e-02 2.50e+03 pdb=" O ALA D 189 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 190 " -0.022 2.00e-02 2.50e+03 ... (remaining 2082 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4770 2.94 - 3.43: 9922 3.43 - 3.92: 13975 3.92 - 4.41: 14059 4.41 - 4.90: 23185 Nonbonded interactions: 65911 Sorted by model distance: nonbonded pdb=" N ASN D 24 " pdb=" O LEU D 43 " model vdw 2.445 3.120 nonbonded pdb=" N ASN B 24 " pdb=" O LEU B 43 " model vdw 2.452 3.120 nonbonded pdb=" N ASN F 24 " pdb=" O LEU F 43 " model vdw 2.453 3.120 nonbonded pdb=" N ASN E 24 " pdb=" O LEU E 43 " model vdw 2.500 3.120 nonbonded pdb=" N ASN A 24 " pdb=" O LEU A 43 " model vdw 2.525 3.120 ... (remaining 65906 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.980 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4695 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 0.054 10317 Z= 0.324 Angle : 1.036 7.510 14346 Z= 0.698 Chirality : 0.057 0.225 1950 Planarity : 0.006 0.041 2085 Dihedral : 5.088 17.788 2088 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 0.20 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 : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2082 helix: -0.55 (0.14), residues: 993 sheet: 0.72 (0.26), residues: 429 loop : -0.99 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.16522 ( 844) hydrogen bonds : angle 7.05731 ( 2451) covalent geometry : bond 0.00457 (10317) covalent geometry : angle 1.03616 (14346) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0920 time to fit residues: 11.8873 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.241882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.233951 restraints weight = 17989.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.224914 restraints weight = 30086.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.223201 restraints weight = 32967.523| |-----------------------------------------------------------------------------| r_work (final): 0.4529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.205 10317 Z= 0.364 Angle : 0.842 13.523 14346 Z= 0.532 Chirality : 0.050 0.188 1950 Planarity : 0.005 0.029 2085 Dihedral : 6.604 27.189 2088 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.46 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2082 helix: -0.42 (0.16), residues: 993 sheet: -0.15 (0.24), residues: 450 loop : -1.34 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.06023 ( 844) hydrogen bonds : angle 6.77595 ( 2451) covalent geometry : bond 0.00583 (10317) covalent geometry : angle 0.84238 (14346) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.302 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0924 time to fit residues: 12.2903 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 73 optimal weight: 50.0000 chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 198 optimal weight: 40.0000 chunk 153 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.231759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.221021 restraints weight = 18468.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.207789 restraints weight = 28213.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.206250 restraints weight = 29668.772| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 10317 Z= 0.401 Angle : 0.890 15.283 14346 Z= 0.567 Chirality : 0.050 0.158 1950 Planarity : 0.006 0.035 2085 Dihedral : 7.515 27.530 2088 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.59 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 2082 helix: -1.58 (0.15), residues: 945 sheet: -0.65 (0.29), residues: 348 loop : -2.23 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.06742 ( 844) hydrogen bonds : angle 7.68203 ( 2451) covalent geometry : bond 0.00573 (10317) covalent geometry : angle 0.89019 (14346) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.661 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0998 time to fit residues: 13.0430 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 140 optimal weight: 30.0000 chunk 198 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.232503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.220877 restraints weight = 18071.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.207961 restraints weight = 24737.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.207268 restraints weight = 28106.927| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 10317 Z= 0.283 Angle : 0.717 13.426 14346 Z= 0.449 Chirality : 0.047 0.142 1950 Planarity : 0.004 0.026 2085 Dihedral : 6.875 27.048 2088 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.18), residues: 2082 helix: -1.24 (0.15), residues: 945 sheet: -0.93 (0.28), residues: 387 loop : -2.22 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05437 ( 844) hydrogen bonds : angle 7.00757 ( 2451) covalent geometry : bond 0.00414 (10317) covalent geometry : angle 0.71651 (14346) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1570 time to fit residues: 20.2521 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 10.0000 chunk 141 optimal weight: 40.0000 chunk 79 optimal weight: 20.0000 chunk 64 optimal weight: 50.0000 chunk 50 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.230069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.219093 restraints weight = 18134.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.203715 restraints weight = 25801.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.202828 restraints weight = 31385.254| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.7743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10317 Z= 0.338 Angle : 0.809 14.695 14346 Z= 0.508 Chirality : 0.048 0.154 1950 Planarity : 0.005 0.028 2085 Dihedral : 7.554 29.588 2088 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.10 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.17), residues: 2082 helix: -1.53 (0.15), residues: 936 sheet: -1.20 (0.29), residues: 360 loop : -2.64 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.06198 ( 844) hydrogen bonds : angle 7.79995 ( 2451) covalent geometry : bond 0.00474 (10317) covalent geometry : angle 0.80891 (14346) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.053 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0980 time to fit residues: 12.5794 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 128 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 184 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.232220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.220526 restraints weight = 17980.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.205373 restraints weight = 24850.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.204414 restraints weight = 28862.849| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.7828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10317 Z= 0.246 Angle : 0.649 13.644 14346 Z= 0.402 Chirality : 0.046 0.138 1950 Planarity : 0.004 0.025 2085 Dihedral : 6.702 25.463 2088 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.18), residues: 2082 helix: -1.08 (0.16), residues: 930 sheet: -1.37 (0.29), residues: 357 loop : -2.65 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 844) hydrogen bonds : angle 7.05575 ( 2451) covalent geometry : bond 0.00348 (10317) covalent geometry : angle 0.64890 (14346) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.418 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1059 time to fit residues: 13.7265 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.226483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.215342 restraints weight = 18268.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.202453 restraints weight = 28288.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.201182 restraints weight = 39671.947| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10317 Z= 0.436 Angle : 0.947 16.718 14346 Z= 0.603 Chirality : 0.051 0.169 1950 Planarity : 0.006 0.033 2085 Dihedral : 8.371 40.606 2088 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.75 % Favored : 85.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.17), residues: 2082 helix: -1.96 (0.15), residues: 912 sheet: -1.40 (0.30), residues: 327 loop : -3.18 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.07400 ( 844) hydrogen bonds : angle 8.69610 ( 2451) covalent geometry : bond 0.00609 (10317) covalent geometry : angle 0.94721 (14346) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.435 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1120 time to fit residues: 14.8569 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 168 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.231103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.219305 restraints weight = 18058.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.204351 restraints weight = 24271.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.203733 restraints weight = 27291.279| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.8611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10317 Z= 0.254 Angle : 0.673 14.137 14346 Z= 0.420 Chirality : 0.046 0.142 1950 Planarity : 0.004 0.025 2085 Dihedral : 7.075 36.804 2088 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.17), residues: 2082 helix: -1.37 (0.16), residues: 918 sheet: -1.29 (0.31), residues: 312 loop : -3.06 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05007 ( 844) hydrogen bonds : angle 7.47749 ( 2451) covalent geometry : bond 0.00358 (10317) covalent geometry : angle 0.67283 (14346) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.351 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1285 time to fit residues: 17.3266 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 199 optimal weight: 40.0000 chunk 103 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 50.0000 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.231493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.221160 restraints weight = 18035.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.218545 restraints weight = 26233.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.217482 restraints weight = 30975.444| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.9054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10317 Z= 0.331 Angle : 0.778 15.296 14346 Z= 0.490 Chirality : 0.048 0.150 1950 Planarity : 0.005 0.027 2085 Dihedral : 7.642 41.760 2088 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.65 % Favored : 85.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.17), residues: 2082 helix: -1.55 (0.16), residues: 912 sheet: -1.39 (0.31), residues: 315 loop : -3.26 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05888 ( 844) hydrogen bonds : angle 8.05802 ( 2451) covalent geometry : bond 0.00466 (10317) covalent geometry : angle 0.77767 (14346) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.414 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2295 time to fit residues: 28.2277 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 181 optimal weight: 0.2980 chunk 41 optimal weight: 0.0000 chunk 203 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.239315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.225213 restraints weight = 17937.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.211210 restraints weight = 27643.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.211017 restraints weight = 26925.213| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.8674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.029 10317 Z= 0.100 Angle : 0.447 9.372 14346 Z= 0.274 Chirality : 0.044 0.143 1950 Planarity : 0.002 0.013 2085 Dihedral : 5.329 25.238 2088 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 2082 helix: 0.06 (0.17), residues: 900 sheet: -1.72 (0.28), residues: 357 loop : -2.59 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.02767 ( 844) hydrogen bonds : angle 5.96236 ( 2451) covalent geometry : bond 0.00141 (10317) covalent geometry : angle 0.44689 (14346) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 2.961 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1960 time to fit residues: 25.1337 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 202 optimal weight: 20.0000 chunk 165 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 194 optimal weight: 40.0000 chunk 140 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.234301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.222757 restraints weight = 17803.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.209643 restraints weight = 27038.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.207268 restraints weight = 32325.485| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.8971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10317 Z= 0.264 Angle : 0.651 12.969 14346 Z= 0.409 Chirality : 0.047 0.141 1950 Planarity : 0.004 0.019 2085 Dihedral : 6.442 30.332 2088 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.18), residues: 2082 helix: -0.46 (0.17), residues: 903 sheet: -1.59 (0.30), residues: 333 loop : -2.89 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 844) hydrogen bonds : angle 7.12996 ( 2451) covalent geometry : bond 0.00373 (10317) covalent geometry : angle 0.65067 (14346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3086.39 seconds wall clock time: 57 minutes 3.25 seconds (3423.25 seconds total)