Starting phenix.real_space_refine on Thu Sep 18 16:59:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6olk_20115/09_2025/6olk_20115.cif Found real_map, /net/cci-nas-00/data/ceres_data/6olk_20115/09_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_20115/09_2025/6olk_20115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6olk_20115/09_2025/6olk_20115.map" model { file = "/net/cci-nas-00/data/ceres_data/6olk_20115/09_2025/6olk_20115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6olk_20115/09_2025/6olk_20115.cif" } resolution = 4.0 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= 0.005 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 15, 'HIS:plan': 11, 'GLN:plan1': 21, 'GLU:plan': 22, 'ARG:plan': 19, 'ASP:plan': 17, 'TYR:plan': 7, 'PHE:plan': 11} 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: {'ASN:plan1': 15, 'HIS:plan': 11, 'GLN:plan1': 21, 'GLU:plan': 22, 'ARG:plan': 19, 'ASP:plan': 17, 'TYR:plan': 7, 'PHE:plan': 11} 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: {'ASN:plan1': 15, 'HIS:plan': 11, 'GLN:plan1': 21, 'GLU:plan': 22, 'ARG:plan': 19, 'ASP:plan': 17, 'TYR:plan': 7, 'PHE:plan': 11} 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: {'ASN:plan1': 15, 'HIS:plan': 11, 'GLN:plan1': 21, 'GLU:plan': 22, 'ARG:plan': 19, 'ASP:plan': 17, 'TYR:plan': 7, 'PHE:plan': 11} 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: {'ASN:plan1': 15, 'HIS:plan': 11, 'GLN:plan1': 21, 'GLU:plan': 22, 'ARG:plan': 19, 'ASP:plan': 17, 'TYR:plan': 7, 'PHE:plan': 11} 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: {'ASN:plan1': 15, 'HIS:plan': 11, 'GLN:plan1': 21, 'GLU:plan': 22, 'ARG:plan': 19, 'ASP:plan': 17, 'TYR:plan': 7, 'PHE:plan': 11} Unresolved non-hydrogen planarities: 533 Time building chain proxies: 2.76, per 1000 atoms: 0.27 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: 1.02 Conformation dependent library (CDL) restraints added in 639.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.47 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: 1.59 Time building geometry restraints manager: 1.23 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: 0.04 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.790 Find NCS groups from input model: 0.090 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.480 ------------------------------------------------------------------------------- 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 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: -0.75 (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 TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00457 (10317) covalent geometry : angle 1.03616 (14346) hydrogen bonds : bond 0.16522 ( 844) hydrogen bonds : angle 7.05731 ( 2451) *********************** 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 : 0.359 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0410 time to fit residues: 5.1262 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 : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 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 = 0.4749 r_free = 0.4749 target = 0.243468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.234664 restraints weight = 18258.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.234050 restraints weight = 30548.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.232288 restraints weight = 30935.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.231106 restraints weight = 38271.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.231242 restraints weight = 38078.830| |-----------------------------------------------------------------------------| r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 10317 Z= 0.316 Angle : 0.779 13.787 14346 Z= 0.485 Chirality : 0.049 0.169 1950 Planarity : 0.005 0.026 2085 Dihedral : 6.461 26.859 2088 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % 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 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: -1.02 (0.17), residues: 2082 helix: -0.36 (0.16), residues: 993 sheet: -0.06 (0.26), residues: 417 loop : -1.32 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00508 (10317) covalent geometry : angle 0.77874 (14346) hydrogen bonds : bond 0.05615 ( 844) hydrogen bonds : angle 6.57132 ( 2451) *********************** 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 : 0.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0442 time to fit residues: 5.4220 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 : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 158 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 130 optimal weight: 30.0000 chunk 164 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 = 0.4673 r_free = 0.4673 target = 0.235151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.223012 restraints weight = 18173.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.210667 restraints weight = 26984.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.210062 restraints weight = 30162.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.209673 restraints weight = 33829.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.209875 restraints weight = 29994.708| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 10317 Z= 0.293 Angle : 0.707 12.973 14346 Z= 0.443 Chirality : 0.048 0.154 1950 Planarity : 0.004 0.022 2085 Dihedral : 6.375 25.102 2088 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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 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: -1.61 (0.17), residues: 2082 helix: -0.65 (0.16), residues: 957 sheet: -0.04 (0.30), residues: 324 loop : -1.92 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00436 (10317) covalent geometry : angle 0.70709 (14346) hydrogen bonds : bond 0.05369 ( 844) hydrogen bonds : angle 6.65055 ( 2451) *********************** 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 : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0395 time to fit residues: 4.8546 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 : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4650 r_free = 0.4650 target = 0.232275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.220452 restraints weight = 18275.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.208196 restraints weight = 27268.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.207311 restraints weight = 40898.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.207607 restraints weight = 38019.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.207785 restraints weight = 33112.289| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 10317 Z= 0.317 Angle : 0.763 13.565 14346 Z= 0.477 Chirality : 0.047 0.149 1950 Planarity : 0.005 0.029 2085 Dihedral : 7.096 29.295 2088 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.59 % Favored : 92.22 % 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 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: -2.14 (0.18), residues: 2082 helix: -1.00 (0.16), residues: 942 sheet: -0.74 (0.29), residues: 375 loop : -2.16 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00453 (10317) covalent geometry : angle 0.76261 (14346) hydrogen bonds : bond 0.05699 ( 844) hydrogen bonds : angle 7.16574 ( 2451) *********************** 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 : 0.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0397 time to fit residues: 4.8908 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 : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 108 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 28 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.4699 r_free = 0.4699 target = 0.237393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.224906 restraints weight = 17984.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.212056 restraints weight = 24888.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.211650 restraints weight = 32114.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.211723 restraints weight = 32870.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.211877 restraints weight = 27180.268| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10317 Z= 0.134 Angle : 0.485 10.744 14346 Z= 0.294 Chirality : 0.044 0.141 1950 Planarity : 0.002 0.012 2085 Dihedral : 5.314 21.641 2088 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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 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: -1.21 (0.19), residues: 2082 helix: 0.09 (0.17), residues: 945 sheet: -0.44 (0.31), residues: 345 loop : -2.01 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00194 (10317) covalent geometry : angle 0.48490 (14346) hydrogen bonds : bond 0.03216 ( 844) hydrogen bonds : angle 5.70729 ( 2451) *********************** 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 : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0406 time to fit residues: 5.0829 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 : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 117 optimal weight: 0.2980 chunk 84 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 139 optimal weight: 20.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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 = 0.4672 r_free = 0.4672 target = 0.234456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.222391 restraints weight = 18319.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.210690 restraints weight = 25541.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.209169 restraints weight = 28508.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.209350 restraints weight = 29801.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.209730 restraints weight = 25312.489| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.6827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10317 Z= 0.206 Angle : 0.568 12.017 14346 Z= 0.350 Chirality : 0.045 0.133 1950 Planarity : 0.003 0.017 2085 Dihedral : 5.781 21.384 2088 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.04 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 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: -1.34 (0.19), residues: 2082 helix: 0.04 (0.17), residues: 948 sheet: -0.71 (0.30), residues: 354 loop : -2.07 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00292 (10317) covalent geometry : angle 0.56846 (14346) hydrogen bonds : bond 0.04072 ( 844) hydrogen bonds : angle 6.25611 ( 2451) *********************** 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 : 0.393 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0420 time to fit residues: 5.2610 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 : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 37 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 131 optimal weight: 50.0000 chunk 46 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 87 optimal weight: 0.0470 chunk 4 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.9884 ------------------------------------------------------------------------------- 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 = 0.4684 r_free = 0.4684 target = 0.235930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.223570 restraints weight = 17957.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 112)---------------| | r_work = 0.4368 r_free = 0.4368 target = 0.209269 restraints weight = 26837.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.207803 restraints weight = 29649.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.207845 restraints weight = 36018.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.207773 restraints weight = 31800.495| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10317 Z= 0.161 Angle : 0.504 11.463 14346 Z= 0.308 Chirality : 0.044 0.140 1950 Planarity : 0.003 0.012 2085 Dihedral : 5.274 20.808 2088 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.57 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 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: -1.09 (0.19), residues: 2082 helix: 0.46 (0.18), residues: 930 sheet: -1.34 (0.27), residues: 414 loop : -1.77 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00228 (10317) covalent geometry : angle 0.50380 (14346) hydrogen bonds : bond 0.03390 ( 844) hydrogen bonds : angle 5.84071 ( 2451) *********************** 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 : 0.357 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0512 time to fit residues: 6.0162 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 : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 199 optimal weight: 5.9990 chunk 193 optimal weight: 0.0980 chunk 178 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 = 0.4674 r_free = 0.4674 target = 0.234963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.222581 restraints weight = 18162.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.210595 restraints weight = 24282.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.209522 restraints weight = 25527.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.209629 restraints weight = 28821.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.209548 restraints weight = 26421.962| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10317 Z= 0.180 Angle : 0.529 11.597 14346 Z= 0.326 Chirality : 0.045 0.131 1950 Planarity : 0.003 0.016 2085 Dihedral : 5.473 20.075 2088 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % 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 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: -1.14 (0.19), residues: 2082 helix: 0.47 (0.18), residues: 930 sheet: -1.50 (0.27), residues: 417 loop : -1.80 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00254 (10317) covalent geometry : angle 0.52936 (14346) hydrogen bonds : bond 0.03705 ( 844) hydrogen bonds : angle 6.05923 ( 2451) *********************** 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 : 0.314 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0460 time to fit residues: 5.5086 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 : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 156 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 197 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 151 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 1.7582 ------------------------------------------------------------------------------- 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 = 0.4700 r_free = 0.4700 target = 0.237781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.225380 restraints weight = 18003.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.214337 restraints weight = 23678.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.212429 restraints weight = 30918.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.212361 restraints weight = 31857.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.212548 restraints weight = 31373.725| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10317 Z= 0.108 Angle : 0.432 10.098 14346 Z= 0.262 Chirality : 0.044 0.132 1950 Planarity : 0.002 0.011 2085 Dihedral : 4.755 19.802 2088 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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 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: -0.71 (0.20), residues: 2082 helix: 0.98 (0.18), residues: 927 sheet: -1.42 (0.27), residues: 414 loop : -1.71 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00153 (10317) covalent geometry : angle 0.43199 (14346) hydrogen bonds : bond 0.02697 ( 844) hydrogen bonds : angle 5.39418 ( 2451) *********************** 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 : 0.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0426 time to fit residues: 5.2911 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4665 r_free = 0.4665 target = 0.233629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.221269 restraints weight = 17909.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.208922 restraints weight = 25310.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.208148 restraints weight = 27720.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.208602 restraints weight = 28339.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.208545 restraints weight = 25644.750| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.7707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10317 Z= 0.208 Angle : 0.566 11.814 14346 Z= 0.352 Chirality : 0.045 0.137 1950 Planarity : 0.003 0.018 2085 Dihedral : 5.630 21.006 2088 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % 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 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: -1.23 (0.19), residues: 2082 helix: 0.49 (0.18), residues: 930 sheet: -1.62 (0.27), residues: 411 loop : -1.94 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00291 (10317) covalent geometry : angle 0.56625 (14346) hydrogen bonds : bond 0.04019 ( 844) hydrogen bonds : angle 6.27908 ( 2451) ********************** 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 : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0442 time to fit residues: 5.4909 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 : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 186 optimal weight: 5.9990 chunk 141 optimal weight: 40.0000 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 chunk 5 optimal weight: 50.0000 chunk 98 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.4681 r_free = 0.4681 target = 0.235678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.223037 restraints weight = 18081.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.210436 restraints weight = 25101.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.209350 restraints weight = 28007.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.209227 restraints weight = 30740.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.209274 restraints weight = 27496.549| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10317 Z= 0.148 Angle : 0.485 10.950 14346 Z= 0.298 Chirality : 0.044 0.134 1950 Planarity : 0.002 0.012 2085 Dihedral : 5.190 20.932 2088 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % 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 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: -1.07 (0.19), residues: 2082 helix: 0.69 (0.18), residues: 930 sheet: -1.62 (0.27), residues: 417 loop : -1.89 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd covalent geometry : bond 0.00210 (10317) covalent geometry : angle 0.48514 (14346) hydrogen bonds : bond 0.03233 ( 844) hydrogen bonds : angle 5.84724 ( 2451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.71 seconds wall clock time: 22 minutes 3.22 seconds (1323.22 seconds total)