Starting phenix.real_space_refine on Thu Sep 18 17:30:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oll_20116/09_2025/6oll_20116.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oll_20116/09_2025/6oll_20116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oll_20116/09_2025/6oll_20116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oll_20116/09_2025/6oll_20116.map" model { file = "/net/cci-nas-00/data/ceres_data/6oll_20116/09_2025/6oll_20116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oll_20116/09_2025/6oll_20116.cif" } resolution = 4.1 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= 0.074 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 10416 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 6198 2.51 5 N 2114 2.21 5 O 2114 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: 10426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 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: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 1731 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1063 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 853 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: "C" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PTRANS': 20, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 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: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 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: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 1731 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1063 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 853 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: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PTRANS': 20, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 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: 3.28, per 1000 atoms: 0.31 Number of scatterers: 10426 At special positions: 0 Unit cell: (124.02, 121.9, 81.62, 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 2114 8.00 N 2114 7.00 C 6198 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: 1.01 Conformation dependent library (CDL) restraints added in 707.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 48.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 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: 4.210A 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 removed outlier: 3.520A pdb=" N TYR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.163A pdb=" N ASP A 197 " --> pdb=" O LEU A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 233 through 244 removed outlier: 3.775A pdb=" N VAL A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) 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 removed outlier: 3.543A pdb=" N PHE A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) 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 352 Processing helix chain 'B' and resid 2 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 113 through 120 removed outlier: 4.142A 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 removed outlier: 3.753A pdb=" N TYR B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) 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 302 through 309 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 341 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 57 through 68 Processing helix chain 'C' and resid 113 through 120 removed outlier: 4.188A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) 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 197 removed outlier: 4.067A pdb=" N ASP C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' 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 310 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 353 Processing helix chain 'D' and resid 2 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 113 through 120 removed outlier: 4.210A 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 removed outlier: 3.511A pdb=" N TYR D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 removed outlier: 4.167A pdb=" N ASP D 197 " --> pdb=" O LEU D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 233 through 244 removed outlier: 3.775A pdb=" N VAL D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 309 Processing helix chain 'D' and resid 310 through 315 removed outlier: 3.542A pdb=" N PHE D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 333 through 341 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'E' and resid 2 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: 4.121A 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 removed outlier: 3.736A pdb=" N TYR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 removed outlier: 4.025A pdb=" N ASP E 197 " --> pdb=" O LEU E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 233 through 244 removed outlier: 3.547A pdb=" N VAL E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 288 through 297 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 113 through 120 removed outlier: 4.202A 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 197 removed outlier: 4.091A pdb=" N ASP F 197 " --> pdb=" O LEU F 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 194 through 197' 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 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 302 through 310 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 341 Processing helix chain 'F' and resid 343 through 353 removed outlier: 3.551A pdb=" N LEU F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 3.653A pdb=" N GLN A 28 " --> pdb=" O HIS A 20 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 30 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 4.797A 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: 6.519A pdb=" N ILE A 156 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 177 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 158 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS A 155 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 202 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 157 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY A 204 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 159 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 203 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR A 228 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU A 205 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 225 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 227 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 126 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU A 265 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A 128 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 267 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 130 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU A 269 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.554A pdb=" N ASP B 18 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 178 removed outlier: 6.543A pdb=" N ILE B 156 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ARG B 177 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 158 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS B 155 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 202 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 157 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY B 204 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 159 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 201 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N THR B 228 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL B 203 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS B 225 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 127 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA B 227 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 129 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 229 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 126 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU B 265 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU B 128 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLN B 267 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR B 130 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU B 269 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 37 removed outlier: 3.718A 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: 6.242A pdb=" N VAL C 201 " --> pdb=" O PHE C 226 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR C 228 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL C 203 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 227 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 229 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU C 126 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU C 265 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU C 128 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN C 267 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR C 130 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU C 269 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.646A pdb=" N GLN D 28 " --> pdb=" O HIS D 20 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 30 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP D 18 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 178 removed outlier: 6.518A pdb=" N ILE D 156 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG D 177 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 158 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS D 155 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU D 202 " --> pdb=" O HIS D 155 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL D 157 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY D 204 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL D 159 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 203 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR D 228 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU D 205 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 225 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 227 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 126 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU D 265 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU D 128 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN D 267 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR D 130 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU D 269 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.631A 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: 6.524A pdb=" N ILE E 156 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ARG E 177 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR E 158 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS E 155 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU E 202 " --> pdb=" O HIS E 155 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL E 157 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY E 204 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL E 159 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 201 " --> pdb=" O PHE E 226 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR E 228 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL E 203 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS E 225 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL E 127 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA E 227 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 129 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 229 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 126 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU E 265 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU E 128 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN E 267 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.048A 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: 3.745A pdb=" N ASP F 18 " --> pdb=" O ARG F 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 173 through 178 removed outlier: 6.208A pdb=" N VAL F 201 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR F 228 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N VAL F 203 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 227 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 229 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU F 126 " --> pdb=" O GLY F 263 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU F 265 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU F 128 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLN F 267 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR F 130 " --> pdb=" O GLN F 267 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU F 269 " --> pdb=" O THR F 130 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2487 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: 1.93 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2114 1.29 - 1.36: 2102 1.36 - 1.42: 4 1.42 - 1.49: 2112 1.49 - 1.55: 4088 Bond restraints: 10420 Sorted by residual: bond pdb=" C ALA E 2 " pdb=" O ALA E 2 " ideal model delta sigma weight residual 1.235 1.263 -0.028 1.26e-02 6.30e+03 5.00e+00 bond pdb=" CA ALA E 2 " pdb=" C ALA E 2 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 3.02e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 ... (remaining 10415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 14030 2.62 - 5.25: 441 5.25 - 7.87: 13 7.87 - 10.49: 4 10.49 - 13.12: 4 Bond angle restraints: 14492 Sorted by residual: angle pdb=" C GLU F 160 " pdb=" N ASP F 161 " pdb=" CA ASP F 161 " ideal model delta sigma weight residual 122.56 130.62 -8.06 1.34e+00 5.57e-01 3.61e+01 angle pdb=" N ASP C 161 " pdb=" CA ASP C 161 " pdb=" C ASP C 161 " ideal model delta sigma weight residual 109.81 96.69 13.12 2.21e+00 2.05e-01 3.52e+01 angle pdb=" N LYS F 103 " pdb=" CA LYS F 103 " pdb=" C LYS F 103 " ideal model delta sigma weight residual 108.73 118.34 -9.61 1.63e+00 3.76e-01 3.47e+01 angle pdb=" N ASP F 161 " pdb=" CA ASP F 161 " pdb=" C ASP F 161 " ideal model delta sigma weight residual 107.91 96.56 11.35 2.05e+00 2.38e-01 3.07e+01 angle pdb=" N LYS C 103 " pdb=" CA LYS C 103 " pdb=" C LYS C 103 " ideal model delta sigma weight residual 109.24 118.08 -8.84 1.63e+00 3.76e-01 2.94e+01 ... (remaining 14487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 6043 21.38 - 42.75: 1 42.75 - 64.13: 0 64.13 - 85.51: 0 85.51 - 106.88: 4 Dihedral angle restraints: 6048 sinusoidal: 0 harmonic: 6048 Sorted by residual: dihedral pdb=" CA ASP B 161 " pdb=" C ASP B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta harmonic sigma weight residual -180.00 -73.12 -106.88 0 5.00e+00 4.00e-02 4.57e+02 dihedral pdb=" CA ASP E 161 " pdb=" C ASP E 161 " pdb=" N PRO E 162 " pdb=" CA PRO E 162 " ideal model delta harmonic sigma weight residual -180.00 -73.37 -106.63 0 5.00e+00 4.00e-02 4.55e+02 dihedral pdb=" CA ASP F 161 " pdb=" C ASP F 161 " pdb=" N PRO F 162 " pdb=" CA PRO F 162 " ideal model delta harmonic sigma weight residual -180.00 -84.19 -95.81 0 5.00e+00 4.00e-02 3.67e+02 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1656 0.076 - 0.151: 284 0.151 - 0.227: 28 0.227 - 0.303: 0 0.303 - 0.378: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CA PRO B 162 " pdb=" N PRO B 162 " pdb=" C PRO B 162 " pdb=" CB PRO B 162 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PRO E 162 " pdb=" N PRO E 162 " pdb=" C PRO E 162 " pdb=" CB PRO E 162 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA LEU F 294 " pdb=" N LEU F 294 " pdb=" C LEU F 294 " pdb=" CB LEU F 294 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1967 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 2 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C ALA B 2 " -0.076 2.00e-02 2.50e+03 pdb=" O ALA B 2 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 3 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 2 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ALA E 2 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA E 2 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN E 3 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 247 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C SER E 247 " -0.060 2.00e-02 2.50e+03 pdb=" O SER E 247 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR E 248 " 0.020 2.00e-02 2.50e+03 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4456 2.90 - 3.40: 9964 3.40 - 3.90: 14393 3.90 - 4.40: 14662 4.40 - 4.90: 24269 Nonbonded interactions: 67744 Sorted by model distance: nonbonded pdb=" N ALA E 273 " pdb=" O HIS E 331 " model vdw 2.400 3.120 nonbonded pdb=" N ALA B 273 " pdb=" O HIS B 331 " model vdw 2.434 3.120 nonbonded pdb=" O GLU E 160 " pdb=" N VAL E 179 " model vdw 2.456 3.120 nonbonded pdb=" N THR A 130 " pdb=" O LEU A 265 " model vdw 2.464 3.120 nonbonded pdb=" O GLU B 160 " pdb=" N VAL B 179 " model vdw 2.465 3.120 ... (remaining 67739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 351) selection = chain 'B' selection = (chain 'C' and resid 1 through 351) selection = (chain 'D' and resid 1 through 351) selection = chain 'E' selection = (chain 'F' and resid 1 through 351) } 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: 1.530 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 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 : 0.004 0.086 10420 Z= 0.302 Angle : 1.052 13.117 14492 Z= 0.702 Chirality : 0.056 0.378 1970 Planarity : 0.005 0.044 2108 Dihedral : 6.943 106.883 2108 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.51 (0.17), residues: 2102 helix: -0.57 (0.14), residues: 990 sheet: 0.99 (0.25), residues: 456 loop : -0.66 (0.22), residues: 656 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 0.00442 (10420) covalent geometry : angle 1.05249 (14492) hydrogen bonds : bond 0.14447 ( 857) hydrogen bonds : angle 7.09085 ( 2487) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0443 time to fit residues: 5.9679 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.0060 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 overall best weight: 4.6004 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.165197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.139906 restraints weight = 34711.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.140875 restraints weight = 30070.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.141750 restraints weight = 22290.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.142060 restraints weight = 19102.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.142343 restraints weight = 17574.471| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10420 Z= 0.253 Angle : 0.641 8.541 14492 Z= 0.415 Chirality : 0.047 0.159 1970 Planarity : 0.004 0.027 2108 Dihedral : 6.505 45.841 2108 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.18), residues: 2102 helix: -0.54 (0.15), residues: 982 sheet: 0.55 (0.26), residues: 436 loop : -0.64 (0.23), residues: 684 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 0.00349 (10420) covalent geometry : angle 0.64140 (14492) hydrogen bonds : bond 0.04892 ( 857) hydrogen bonds : angle 5.94529 ( 2487) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.537 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0395 time to fit residues: 5.3983 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 198 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 208 optimal weight: 0.0170 chunk 139 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 overall best weight: 2.1824 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.166568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.141595 restraints weight = 34929.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.141743 restraints weight = 28631.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.142692 restraints weight = 22456.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.143169 restraints weight = 19221.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.143338 restraints weight = 17573.306| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10420 Z= 0.122 Angle : 0.429 6.105 14492 Z= 0.275 Chirality : 0.044 0.146 1970 Planarity : 0.002 0.013 2108 Dihedral : 4.860 30.374 2108 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.22 (0.19), residues: 2102 helix: 0.56 (0.16), residues: 1000 sheet: 0.51 (0.26), residues: 452 loop : -0.57 (0.25), residues: 650 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 0.00182 (10420) covalent geometry : angle 0.42923 (14492) hydrogen bonds : bond 0.03128 ( 857) hydrogen bonds : angle 5.09787 ( 2487) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0434 time to fit residues: 5.8105 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 30.0000 chunk 86 optimal weight: 30.0000 chunk 142 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.154315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.129928 restraints weight = 34441.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.130283 restraints weight = 25694.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.130897 restraints weight = 20972.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131213 restraints weight = 17795.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.131400 restraints weight = 16598.754| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10420 Z= 0.360 Angle : 0.756 6.435 14492 Z= 0.496 Chirality : 0.048 0.173 1970 Planarity : 0.005 0.023 2108 Dihedral : 6.977 25.003 2108 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.95 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -2.55 (0.17), residues: 2102 helix: -1.71 (0.14), residues: 970 sheet: -0.15 (0.27), residues: 388 loop : -2.31 (0.21), residues: 744 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 0.00497 (10420) covalent geometry : angle 0.75622 (14492) hydrogen bonds : bond 0.06465 ( 857) hydrogen bonds : angle 7.47227 ( 2487) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0449 time to fit residues: 6.0462 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 100 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.151530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.126861 restraints weight = 35152.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.126904 restraints weight = 26739.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.127597 restraints weight = 22132.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.127889 restraints weight = 19141.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.128048 restraints weight = 17951.176| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10420 Z= 0.295 Angle : 0.643 5.332 14492 Z= 0.425 Chirality : 0.046 0.148 1970 Planarity : 0.004 0.028 2108 Dihedral : 6.396 22.216 2108 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.47 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -3.19 (0.17), residues: 2102 helix: -2.13 (0.14), residues: 960 sheet: -0.56 (0.26), residues: 438 loop : -2.88 (0.23), residues: 704 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 0.00415 (10420) covalent geometry : angle 0.64257 (14492) hydrogen bonds : bond 0.05525 ( 857) hydrogen bonds : angle 7.43058 ( 2487) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0460 time to fit residues: 6.2728 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 176 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 134 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.156709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.131689 restraints weight = 36013.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.131912 restraints weight = 27943.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.132524 restraints weight = 23019.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.132678 restraints weight = 21194.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.132933 restraints weight = 18917.926| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10420 Z= 0.249 Angle : 0.578 5.111 14492 Z= 0.382 Chirality : 0.045 0.157 1970 Planarity : 0.004 0.030 2108 Dihedral : 5.920 23.060 2108 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -3.10 (0.17), residues: 2102 helix: -1.74 (0.14), residues: 960 sheet: -0.81 (0.27), residues: 412 loop : -3.07 (0.23), residues: 730 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 0.00348 (10420) covalent geometry : angle 0.57758 (14492) hydrogen bonds : bond 0.05002 ( 857) hydrogen bonds : angle 7.12068 ( 2487) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.467 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0457 time to fit residues: 6.1769 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 115 optimal weight: 20.0000 chunk 208 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 134 optimal weight: 30.0000 overall best weight: 3.9784 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.158042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.132608 restraints weight = 35279.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.133320 restraints weight = 26720.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.134252 restraints weight = 20836.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.134371 restraints weight = 18077.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.134721 restraints weight = 16587.318| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.7927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10420 Z= 0.181 Angle : 0.496 4.539 14492 Z= 0.325 Chirality : 0.044 0.131 1970 Planarity : 0.003 0.011 2108 Dihedral : 5.364 18.199 2108 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -2.77 (0.18), residues: 2102 helix: -1.31 (0.15), residues: 968 sheet: -1.03 (0.26), residues: 422 loop : -2.92 (0.23), residues: 712 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 0.00249 (10420) covalent geometry : angle 0.49601 (14492) hydrogen bonds : bond 0.04068 ( 857) hydrogen bonds : angle 6.71762 ( 2487) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.410 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0439 time to fit residues: 5.9299 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 84 optimal weight: 0.5980 chunk 169 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 201 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 overall best weight: 6.7188 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.153691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.129141 restraints weight = 35933.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.128994 restraints weight = 27909.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.129942 restraints weight = 23286.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.129927 restraints weight = 20641.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.130150 restraints weight = 19115.570| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.8615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10420 Z= 0.299 Angle : 0.655 5.285 14492 Z= 0.434 Chirality : 0.047 0.163 1970 Planarity : 0.004 0.016 2108 Dihedral : 6.445 30.876 2108 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.37 % Favored : 84.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.56 (0.17), residues: 2102 helix: -2.14 (0.14), residues: 956 sheet: -1.18 (0.26), residues: 426 loop : -3.18 (0.23), residues: 720 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 0.00416 (10420) covalent geometry : angle 0.65531 (14492) hydrogen bonds : bond 0.05855 ( 857) hydrogen bonds : angle 7.65653 ( 2487) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.394 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0461 time to fit residues: 6.2383 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 104 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 50.0000 chunk 154 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4442 r_free = 0.4442 target = 0.159664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.133952 restraints weight = 35139.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.134723 restraints weight = 27014.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.135784 restraints weight = 20966.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.136033 restraints weight = 17872.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.136256 restraints weight = 17001.212| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.8418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 10420 Z= 0.120 Angle : 0.431 4.025 14492 Z= 0.281 Chirality : 0.044 0.131 1970 Planarity : 0.002 0.008 2108 Dihedral : 4.889 17.660 2108 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -2.43 (0.18), residues: 2102 helix: -0.71 (0.15), residues: 966 sheet: -1.38 (0.26), residues: 426 loop : -2.90 (0.24), residues: 710 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 0.00163 (10420) covalent geometry : angle 0.43132 (14492) hydrogen bonds : bond 0.03270 ( 857) hydrogen bonds : angle 6.34981 ( 2487) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0463 time to fit residues: 6.2647 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 50.0000 chunk 170 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.152979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.128938 restraints weight = 35629.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.128323 restraints weight = 27724.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.129124 restraints weight = 23064.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.129368 restraints weight = 20031.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.129518 restraints weight = 18775.911| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.8993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10420 Z= 0.310 Angle : 0.654 5.428 14492 Z= 0.434 Chirality : 0.047 0.164 1970 Planarity : 0.004 0.015 2108 Dihedral : 6.303 30.254 2108 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.57 (0.17), residues: 2102 helix: -2.03 (0.14), residues: 968 sheet: -1.47 (0.26), residues: 422 loop : -3.18 (0.23), residues: 712 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 0.00430 (10420) covalent geometry : angle 0.65399 (14492) hydrogen bonds : bond 0.05928 ( 857) hydrogen bonds : angle 7.61054 ( 2487) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.411 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0463 time to fit residues: 6.2841 Evaluate side-chains 66 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 36 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 148 optimal weight: 30.0000 chunk 199 optimal weight: 0.0770 chunk 149 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 overall best weight: 4.2146 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.155313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.130348 restraints weight = 35551.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.130535 restraints weight = 26813.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.131361 restraints weight = 22230.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.131566 restraints weight = 19859.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.131739 restraints weight = 18151.428| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.8993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10420 Z= 0.194 Angle : 0.516 4.955 14492 Z= 0.339 Chirality : 0.045 0.133 1970 Planarity : 0.003 0.012 2108 Dihedral : 5.528 20.236 2108 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -3.16 (0.18), residues: 2102 helix: -1.53 (0.14), residues: 970 sheet: -1.51 (0.26), residues: 418 loop : -3.05 (0.24), residues: 714 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 0.00265 (10420) covalent geometry : angle 0.51566 (14492) hydrogen bonds : bond 0.04354 ( 857) hydrogen bonds : angle 6.96806 ( 2487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1421.66 seconds wall clock time: 24 minutes 54.38 seconds (1494.38 seconds total)