Starting phenix.real_space_refine (version: dev) on Sat May 14 18:30:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olk_20115/05_2022/6olk_20115.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olk_20115/05_2022/6olk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olk_20115/05_2022/6olk_20115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olk_20115/05_2022/6olk_20115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olk_20115/05_2022/6olk_20115.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olk_20115/05_2022/6olk_20115.pdb" } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 19, 'TRANS': 328, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 328, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 328, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 328, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 328, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 328, 'PCIS': 1} 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: 7.05, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 4.20 Conformation dependent library (CDL) restraints added in 2.3 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: 1.48 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: 3.66 Time building geometry restraints manager: 4.54 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: 101.27 - 107.72: 334 107.72 - 114.17: 5517 114.17 - 120.62: 4180 120.62 - 127.07: 4309 127.07 - 133.52: 6 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 2.520 nonbonded pdb=" N ASN B 24 " pdb=" O LEU B 43 " model vdw 2.452 2.520 nonbonded pdb=" N ASN F 24 " pdb=" O LEU F 43 " model vdw 2.453 2.520 nonbonded pdb=" N ASN E 24 " pdb=" O LEU E 43 " model vdw 2.500 2.520 nonbonded pdb=" N ASN A 24 " pdb=" O LEU A 43 " model vdw 2.525 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 350) selection = (chain 'B' and (resid 3 through 271 or (resid 272 and (name N or name CA or name \ C or name CB )) or resid 273 through 350)) selection = (chain 'C' and resid 3 through 350) selection = (chain 'D' and (resid 3 through 271 or (resid 272 and (name N or name CA or name \ C or name CB )) or resid 273 through 350)) selection = (chain 'E' and resid 3 through 350) selection = (chain 'F' and (resid 3 through 271 or (resid 272 and (name N or name CA or name \ C or name CB )) or resid 273 through 350)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 0.640 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: 4.330 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.090 Process input model: 32.620 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4898 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= 0.337 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.105 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0902 time to fit residues: 11.8754 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4431 ------------------------------------------------------------------------------- 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: 10.0000 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 61 optimal weight: 50.0000 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.183 10317 Z= 0.398 Angle : 0.817 14.947 14346 Z= 0.506 Chirality : 0.049 0.179 1950 Planarity : 0.005 0.029 2085 Dihedral : 6.801 27.653 2088 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer Outliers : 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: -1.36 (0.17), residues: 2082 helix: -0.67 (0.15), residues: 990 sheet: -0.20 (0.25), residues: 417 loop : -1.45 (0.21), residues: 675 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0909 time to fit residues: 11.9072 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 165 optimal weight: 30.0000 chunk 184 optimal weight: 0.5980 chunk 63 optimal weight: 50.0000 chunk 148 optimal weight: 0.0060 overall best weight: 4.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5462 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 10317 Z= 0.265 Angle : 0.599 10.939 14346 Z= 0.376 Chirality : 0.046 0.151 1950 Planarity : 0.003 0.016 2085 Dihedral : 5.561 19.941 2088 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 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: -0.88 (0.18), residues: 2082 helix: 0.06 (0.17), residues: 939 sheet: -0.01 (0.28), residues: 372 loop : -1.59 (0.21), residues: 771 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.169 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0908 time to fit residues: 11.8886 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 197 optimal weight: 50.0000 chunk 97 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 10317 Z= 0.192 Angle : 0.512 10.647 14346 Z= 0.314 Chirality : 0.044 0.132 1950 Planarity : 0.003 0.013 2085 Dihedral : 5.208 18.792 2088 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 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: -0.47 (0.19), residues: 2082 helix: 0.63 (0.17), residues: 936 sheet: -0.12 (0.29), residues: 360 loop : -1.51 (0.22), residues: 786 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0937 time to fit residues: 12.3699 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 10317 Z= 0.420 Angle : 0.878 13.674 14346 Z= 0.562 Chirality : 0.051 0.179 1950 Planarity : 0.006 0.026 2085 Dihedral : 7.215 27.758 2088 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer Outliers : 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: -2.31 (0.18), residues: 2082 helix: -1.10 (0.16), residues: 939 sheet: -0.96 (0.28), residues: 384 loop : -2.21 (0.22), residues: 759 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0925 time to fit residues: 12.2160 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 50.0000 chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 10317 Z= 0.181 Angle : 0.535 11.707 14346 Z= 0.328 Chirality : 0.044 0.137 1950 Planarity : 0.003 0.015 2085 Dihedral : 5.701 21.279 2088 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 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: -1.51 (0.19), residues: 2082 helix: -0.12 (0.17), residues: 939 sheet: -1.18 (0.28), residues: 402 loop : -1.90 (0.24), residues: 741 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0955 time to fit residues: 12.6029 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 166 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10317 Z= 0.253 Angle : 0.635 12.985 14346 Z= 0.395 Chirality : 0.046 0.141 1950 Planarity : 0.004 0.019 2085 Dihedral : 6.291 22.663 2088 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.82 % Favored : 88.14 % Rotamer Outliers : 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: -1.72 (0.19), residues: 2082 helix: -0.19 (0.17), residues: 921 sheet: -1.22 (0.28), residues: 387 loop : -2.18 (0.23), residues: 774 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.153 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0920 time to fit residues: 12.0107 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10317 Z= 0.242 Angle : 0.609 13.014 14346 Z= 0.380 Chirality : 0.046 0.140 1950 Planarity : 0.004 0.017 2085 Dihedral : 6.148 23.612 2088 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer Outliers : 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: -1.88 (0.19), residues: 2082 helix: -0.24 (0.17), residues: 921 sheet: -1.19 (0.29), residues: 363 loop : -2.42 (0.22), residues: 798 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.166 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0943 time to fit residues: 12.4180 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 165 optimal weight: 30.0000 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.8048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10317 Z= 0.257 Angle : 0.634 13.254 14346 Z= 0.396 Chirality : 0.046 0.137 1950 Planarity : 0.004 0.019 2085 Dihedral : 6.365 24.307 2088 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.49 % Favored : 87.46 % Rotamer Outliers : 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: -2.04 (0.19), residues: 2082 helix: -0.33 (0.17), residues: 918 sheet: -1.38 (0.28), residues: 381 loop : -2.50 (0.22), residues: 783 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.065 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0929 time to fit residues: 12.1544 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 30.0000 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5623 moved from start: 0.8158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10317 Z= 0.213 Angle : 0.566 12.414 14346 Z= 0.352 Chirality : 0.045 0.136 1950 Planarity : 0.003 0.017 2085 Dihedral : 5.937 23.570 2088 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer Outliers : 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: -1.83 (0.19), residues: 2082 helix: -0.03 (0.17), residues: 915 sheet: -1.30 (0.29), residues: 363 loop : -2.53 (0.22), residues: 804 ********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0951 time to fit residues: 12.2894 Evaluate side-chains 60 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 49 optimal weight: 0.0170 chunk 149 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 67 optimal weight: 50.0000 chunk 166 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 overall best weight: 1.7224 ------------------------------------------------------------------------------- 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 = 0.4694 r_free = 0.4694 target = 0.237443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.223163 restraints weight = 17765.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.212581 restraints weight = 26565.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.211929 restraints weight = 26536.788| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10317 Z= 0.121 Angle : 0.439 10.403 14346 Z= 0.268 Chirality : 0.044 0.131 1950 Planarity : 0.002 0.013 2085 Dihedral : 4.929 19.971 2088 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 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: -1.09 (0.19), residues: 2082 helix: 0.77 (0.18), residues: 918 sheet: -1.56 (0.26), residues: 426 loop : -2.06 (0.24), residues: 738 =============================================================================== Job complete usr+sys time: 1295.05 seconds wall clock time: 23 minutes 59.67 seconds (1439.67 seconds total)