Starting phenix.real_space_refine on Sat Sep 12 23:25:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6olm_20117/09_2026/6olm_20117.cif Found real_map, /net/cci-nas-00/data/ceres_data/6olm_20117/09_2026/6olm_20117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6olm_20117/09_2026/6olm_20117.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6olm_20117/09_2026/6olm_20117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6olm_20117/09_2026/6olm_20117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6olm_20117/09_2026/6olm_20117.map" model { file = "/net/cci-nas-00/data/ceres_data/6olm_20117/09_2026/6olm_20117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6olm_20117/09_2026/6olm_20117.cif" } resolution = 4.4 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= 0.001 sd= 0.043 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 10596 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: 4 Type Number sf(0) Gaussians P 18 5.49 5 C 6252 2.51 5 N 2142 2.21 5 O 2190 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 1736 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 310} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 331} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1065 Unresolved non-hydrogen angles: 1361 Unresolved non-hydrogen dihedrals: 854 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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.79, per 1000 atoms: 0.17 Number of scatterers: 10602 At special positions: 0 Unit cell: (126.15, 117.45, 73.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 18 15.00 O 2190 8.00 N 2142 7.00 C 6252 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: 1.06 Conformation dependent library (CDL) restraints added in 723.6 milliseconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 50.3% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 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 106 through 111 Processing helix chain 'A' and resid 113 through 120 removed outlier: 4.283A 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 194 removed outlier: 4.713A pdb=" N LEU A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' 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 310 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 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 106 through 111 Processing helix chain 'B' and resid 113 through 120 removed outlier: 4.283A 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 197 removed outlier: 4.022A pdb=" N ASP B 197 " --> pdb=" O LEU B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 288 through 297 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 302 through 310 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 352 Processing helix chain 'C' and resid 2 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 106 through 111 Processing helix chain 'C' and resid 113 through 120 removed outlier: 4.283A 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: 4.023A 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 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 352 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 106 through 111 Processing helix chain 'D' and resid 113 through 120 removed outlier: 4.283A 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 194 removed outlier: 4.713A pdb=" N LEU D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' 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 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 310 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 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: 4.284A 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 194 removed outlier: 4.713A pdb=" N LEU E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 233 through 244 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 310 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 352 Processing helix chain 'F' and resid 2 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: 4.283A 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 194 removed outlier: 4.712A pdb=" N LEU F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 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 352 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 178 removed outlier: 6.387A pdb=" N ILE A 156 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG A 177 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR A 158 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS A 155 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU A 202 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 157 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY A 204 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL A 159 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A 228 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU A 205 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLY A 125 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA A 227 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 127 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU A 229 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 129 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 126 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU A 265 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 128 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN A 267 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR A 130 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 7.849A 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 Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 178 removed outlier: 6.387A pdb=" N ILE B 156 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG B 177 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR B 158 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS B 155 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU B 202 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 157 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY B 204 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL B 159 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B 228 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU B 205 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLY B 125 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA B 227 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 127 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU B 229 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 129 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 126 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 265 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 128 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLN B 267 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR B 130 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 7.849A 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 Processing sheet with id=AA6, first strand: chain 'C' and resid 173 through 178 removed outlier: 6.387A pdb=" N ILE C 156 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG C 177 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR C 158 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N HIS C 155 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU C 202 " --> pdb=" O HIS C 155 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 157 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY C 204 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL C 159 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C 228 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU C 205 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLY C 125 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ALA C 227 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 127 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU C 229 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 129 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU C 126 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU C 265 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU C 128 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN C 267 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR C 130 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 7.849A 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 Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 178 removed outlier: 6.387A pdb=" N ILE D 156 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG D 177 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR D 158 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS D 155 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU D 202 " --> pdb=" O HIS D 155 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 157 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY D 204 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL D 159 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR D 228 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU D 205 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLY D 125 " --> pdb=" O CYS D 225 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA D 227 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL D 127 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU D 229 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 129 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU D 126 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU D 265 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU D 128 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN D 267 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR D 130 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 7.849A 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 Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.387A pdb=" N ILE E 156 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG E 177 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR E 158 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS E 155 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU E 202 " --> pdb=" O HIS E 155 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL E 157 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY E 204 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL E 159 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR E 228 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU E 205 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLY E 125 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA E 227 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL E 127 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU E 229 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL E 129 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU E 126 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU E 265 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU E 128 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN E 267 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR E 130 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 7.849A 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 Processing sheet with id=AB3, first strand: chain 'F' and resid 173 through 178 removed outlier: 6.387A pdb=" N ILE F 156 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG F 177 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR F 158 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS F 155 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU F 202 " --> pdb=" O HIS F 155 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 157 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY F 204 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL F 159 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR F 228 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU F 205 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLY F 125 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA F 227 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL F 127 " --> pdb=" O ALA F 227 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU F 229 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL F 129 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU F 126 " --> pdb=" O GLY F 263 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU F 265 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU F 128 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN F 267 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR F 130 " --> pdb=" O GLN F 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU F 269 " --> pdb=" O THR F 130 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2541 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: 2.07 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.32: 2132 1.32 - 1.41: 2170 1.41 - 1.51: 2332 1.51 - 1.61: 3950 1.61 - 1.70: 24 Bond restraints: 10608 Sorted by residual: bond pdb=" C1' ATP E 401 " pdb=" C2' ATP E 401 " ideal model delta sigma weight residual 1.531 1.286 0.245 1.20e-02 6.94e+03 4.18e+02 bond pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " ideal model delta sigma weight residual 1.531 1.286 0.245 1.20e-02 6.94e+03 4.18e+02 bond pdb=" C1' ATP D 401 " pdb=" C2' ATP D 401 " ideal model delta sigma weight residual 1.531 1.286 0.245 1.20e-02 6.94e+03 4.17e+02 bond pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " ideal model delta sigma weight residual 1.531 1.286 0.245 1.20e-02 6.94e+03 4.17e+02 bond pdb=" C1' ATP C 401 " pdb=" C2' ATP C 401 " ideal model delta sigma weight residual 1.531 1.286 0.245 1.20e-02 6.94e+03 4.16e+02 ... (remaining 10603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 14642 4.05 - 8.10: 112 8.10 - 12.15: 24 12.15 - 16.21: 6 16.21 - 20.26: 6 Bond angle restraints: 14790 Sorted by residual: angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 119.61 20.26 1.00e+00 1.00e+00 4.10e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 119.62 20.25 1.00e+00 1.00e+00 4.10e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 119.64 20.23 1.00e+00 1.00e+00 4.09e+02 angle pdb=" PB ATP D 401 " pdb=" O3B ATP D 401 " pdb=" PG ATP D 401 " ideal model delta sigma weight residual 139.87 119.64 20.23 1.00e+00 1.00e+00 4.09e+02 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 119.70 20.17 1.00e+00 1.00e+00 4.07e+02 ... (remaining 14785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 6036 16.11 - 32.22: 18 32.22 - 48.33: 0 48.33 - 64.44: 0 64.44 - 80.54: 6 Dihedral angle restraints: 6060 sinusoidal: 18 harmonic: 6042 Sorted by residual: dihedral pdb=" CA CYS F 172 " pdb=" C CYS F 172 " pdb=" N VAL F 173 " pdb=" CA VAL F 173 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA CYS E 172 " pdb=" C CYS E 172 " pdb=" N VAL E 173 " pdb=" CA VAL E 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 CYS A 172 " pdb=" C CYS A 172 " pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1427 0.059 - 0.119: 455 0.119 - 0.178: 104 0.178 - 0.238: 0 0.238 - 0.297: 6 Chirality restraints: 1992 Sorted by residual: chirality pdb=" C2' ATP E 401 " pdb=" C1' ATP E 401 " pdb=" C3' ATP E 401 " pdb=" O2' ATP E 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2' ATP A 401 " pdb=" C1' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O2' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' ATP D 401 " pdb=" C1' ATP D 401 " pdb=" C3' ATP D 401 " pdb=" O2' ATP D 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.39 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1989 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D 350 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C MET D 350 " 0.063 2.00e-02 2.50e+03 pdb=" O MET D 350 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 351 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 350 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C MET C 350 " 0.063 2.00e-02 2.50e+03 pdb=" O MET C 350 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU C 351 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 350 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C MET A 350 " 0.063 2.00e-02 2.50e+03 pdb=" O MET A 350 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU A 351 " -0.021 2.00e-02 2.50e+03 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5099 2.93 - 3.42: 10836 3.42 - 3.92: 14974 3.92 - 4.41: 16465 4.41 - 4.90: 25630 Nonbonded interactions: 73004 Sorted by model distance: nonbonded pdb=" N SER C 138 " pdb=" O1B ATP C 401 " model vdw 2.439 3.120 nonbonded pdb=" N SER A 138 " pdb=" O1B ATP A 401 " model vdw 2.440 3.120 nonbonded pdb=" N SER D 138 " pdb=" O1B ATP D 401 " model vdw 2.440 3.120 nonbonded pdb=" N SER E 138 " pdb=" O1B ATP E 401 " model vdw 2.440 3.120 nonbonded pdb=" N SER B 138 " pdb=" O1B ATP B 401 " model vdw 2.441 3.120 ... (remaining 72999 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.012 0.245 10608 Z= 0.969 Angle : 1.281 20.257 14790 Z= 0.975 Chirality : 0.060 0.297 1992 Planarity : 0.006 0.036 2112 Dihedral : 6.940 80.545 2124 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2100 helix: -0.39 (0.14), residues: 996 sheet: 0.80 (0.24), residues: 480 loop : -0.45 (0.22), residues: 624 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/Z covalent geometry : bond 0.01212 / 0.97 (10608) covalent geometry : angle 1.28068 / 0.97 (14790) hydrogen bonds : bond 0.14045 / 10.87 ( 877) hydrogen bonds : angle 7.45570 / 5.71 ( 2541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.372 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0468 time to fit residues: 6.3418 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 30.0000 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.051210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.042089 restraints weight = 110866.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.042510 restraints weight = 98008.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.042857 restraints weight = 89402.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.043155 restraints weight = 82198.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.043441 restraints weight = 76593.992| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10608 Z= 0.242 Angle : 0.552 5.320 14790 Z= 0.351 Chirality : 0.045 0.141 1992 Planarity : 0.003 0.012 2112 Dihedral : 6.821 89.598 2124 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.81 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 2100 helix: 1.15 (0.17), residues: 1014 sheet: 1.10 (0.26), residues: 420 loop : 0.16 (0.24), residues: 666 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/Z covalent geometry : bond 0.00362 / 0.24 (10608) covalent geometry : angle 0.55224 / 0.35 (14790) hydrogen bonds : bond 0.05159 / 3.99 ( 877) hydrogen bonds : angle 5.50171 / 4.22 ( 2541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0468 time to fit residues: 6.2315 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 57 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 182 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 chunk 52 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 199 optimal weight: 40.0000 chunk 34 optimal weight: 0.2980 overall best weight: 8.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.043993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.035998 restraints weight = 120689.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036384 restraints weight = 104388.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.036781 restraints weight = 93834.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.037070 restraints weight = 84896.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037319 restraints weight = 78505.410| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10608 Z= 0.434 Angle : 0.756 7.390 14790 Z= 0.484 Chirality : 0.046 0.148 1992 Planarity : 0.005 0.018 2112 Dihedral : 8.218 77.238 2124 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.17), residues: 2100 helix: -0.54 (0.15), residues: 942 sheet: -0.21 (0.26), residues: 384 loop : -0.83 (0.21), residues: 774 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/Z covalent geometry : bond 0.00631 / 0.43 (10608) covalent geometry : angle 0.75631 / 0.48 (14790) hydrogen bonds : bond 0.06809 / 5.27 ( 877) hydrogen bonds : angle 7.08059 / 5.44 ( 2541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.463 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0462 time to fit residues: 6.2139 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 149 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.044841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.036703 restraints weight = 119760.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.037116 restraints weight = 104849.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.037401 restraints weight = 94149.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.037702 restraints weight = 86716.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037900 restraints weight = 80702.276| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10608 Z= 0.162 Angle : 0.411 3.166 14790 Z= 0.270 Chirality : 0.043 0.142 1992 Planarity : 0.002 0.009 2112 Dihedral : 7.331 82.051 2124 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 2100 helix: 1.04 (0.16), residues: 1014 sheet: -0.56 (0.25), residues: 414 loop : -0.30 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.16 (10608) covalent geometry : angle 0.41068 / 0.27 (14790) hydrogen bonds : bond 0.03424 / 2.67 ( 877) hydrogen bonds : angle 5.52703 / 4.22 ( 2541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.513 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0455 time to fit residues: 6.2403 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 164 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 96 optimal weight: 40.0000 chunk 186 optimal weight: 0.9980 chunk 188 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 74 optimal weight: 0.4980 chunk 87 optimal weight: 40.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.044663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.036506 restraints weight = 118733.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.036920 restraints weight = 104366.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.037254 restraints weight = 94219.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.037531 restraints weight = 86334.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.037685 restraints weight = 80240.302| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10608 Z= 0.150 Angle : 0.386 2.700 14790 Z= 0.251 Chirality : 0.043 0.143 1992 Planarity : 0.002 0.007 2112 Dihedral : 7.132 77.996 2124 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 2100 helix: 2.07 (0.17), residues: 1026 sheet: -0.70 (0.26), residues: 414 loop : -0.29 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 53 PHE 0.000 0.000 PHE A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.15 (10608) covalent geometry : angle 0.38587 / 0.25 (14790) hydrogen bonds : bond 0.02851 / 2.21 ( 877) hydrogen bonds : angle 4.92331 / 3.77 ( 2541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.417 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0466 time to fit residues: 6.3697 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 73 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 173 optimal weight: 8.9990 chunk 82 optimal weight: 0.4980 chunk 78 optimal weight: 30.0000 chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 50.0000 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.032838 restraints weight = 124349.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.033276 restraints weight = 106597.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.033659 restraints weight = 94445.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.033969 restraints weight = 85434.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.034218 restraints weight = 78844.404| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10608 Z= 0.207 Angle : 0.445 4.101 14790 Z= 0.290 Chirality : 0.043 0.139 1992 Planarity : 0.002 0.009 2112 Dihedral : 7.633 82.595 2124 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 2100 helix: 1.73 (0.17), residues: 1032 sheet: -1.06 (0.25), residues: 432 loop : -0.20 (0.25), residues: 636 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/Z covalent geometry : bond 0.00318 / 0.21 (10608) covalent geometry : angle 0.44548 / 0.29 (14790) hydrogen bonds : bond 0.03463 / 2.69 ( 877) hydrogen bonds : angle 5.40880 / 4.15 ( 2541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.444 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0481 time to fit residues: 6.5069 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 164 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 186 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 206 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 146 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 overall best weight: 5.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.042727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.035020 restraints weight = 120940.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.035322 restraints weight = 107076.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035652 restraints weight = 97256.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.035915 restraints weight = 90002.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.036097 restraints weight = 83690.490| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10608 Z= 0.254 Angle : 0.492 3.936 14790 Z= 0.321 Chirality : 0.044 0.145 1992 Planarity : 0.003 0.011 2112 Dihedral : 7.664 87.841 2124 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 2100 helix: 1.23 (0.17), residues: 1026 sheet: -1.45 (0.28), residues: 360 loop : -0.71 (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/Z covalent geometry : bond 0.00373 / 0.25 (10608) covalent geometry : angle 0.49161 / 0.32 (14790) hydrogen bonds : bond 0.04074 / 3.15 ( 877) hydrogen bonds : angle 5.95354 / 4.58 ( 2541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.412 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0525 time to fit residues: 6.9344 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 5 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 96 optimal weight: 40.0000 chunk 152 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 3 optimal weight: 7.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.042920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.035180 restraints weight = 119181.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.035502 restraints weight = 105179.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.035845 restraints weight = 95239.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.036032 restraints weight = 87762.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.036311 restraints weight = 82433.220| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.8010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10608 Z= 0.212 Angle : 0.450 3.871 14790 Z= 0.295 Chirality : 0.043 0.143 1992 Planarity : 0.002 0.009 2112 Dihedral : 7.289 86.386 2124 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 2100 helix: 1.31 (0.17), residues: 1032 sheet: -1.56 (0.27), residues: 360 loop : -0.60 (0.24), residues: 708 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/Z covalent geometry : bond 0.00323 / 0.21 (10608) covalent geometry : angle 0.45047 / 0.29 (14790) hydrogen bonds : bond 0.03570 / 2.77 ( 877) hydrogen bonds : angle 5.76776 / 4.44 ( 2541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.452 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0479 time to fit residues: 6.4594 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 57 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 137 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.042417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034753 restraints weight = 120362.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.035072 restraints weight = 105472.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.035352 restraints weight = 95883.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035701 restraints weight = 87871.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.035915 restraints weight = 80935.877| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.8555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10608 Z= 0.222 Angle : 0.464 4.019 14790 Z= 0.303 Chirality : 0.043 0.146 1992 Planarity : 0.003 0.010 2112 Dihedral : 6.732 76.303 2124 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 2100 helix: 1.33 (0.17), residues: 1026 sheet: -1.85 (0.27), residues: 360 loop : -0.72 (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/Z covalent geometry : bond 0.00331 / 0.22 (10608) covalent geometry : angle 0.46376 / 0.30 (14790) hydrogen bonds : bond 0.03682 / 2.85 ( 877) hydrogen bonds : angle 5.83402 / 4.50 ( 2541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.436 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0465 time to fit residues: 6.3159 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 173 optimal weight: 30.0000 chunk 127 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 54 optimal weight: 0.0470 chunk 154 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 152 optimal weight: 30.0000 chunk 104 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 30.0000 chunk 4 optimal weight: 0.7980 overall best weight: 4.9686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.042308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.034675 restraints weight = 120216.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034979 restraints weight = 105955.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.035324 restraints weight = 96004.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.035558 restraints weight = 87925.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.035787 restraints weight = 82007.955| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.8857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10608 Z= 0.226 Angle : 0.462 3.804 14790 Z= 0.304 Chirality : 0.043 0.150 1992 Planarity : 0.002 0.009 2112 Dihedral : 6.463 71.640 2124 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 2100 helix: 1.28 (0.17), residues: 1026 sheet: -2.25 (0.27), residues: 330 loop : -0.75 (0.23), 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/Z covalent geometry : bond 0.00338 / 0.23 (10608) covalent geometry : angle 0.46169 / 0.30 (14790) hydrogen bonds : bond 0.03677 / 2.84 ( 877) hydrogen bonds : angle 5.90990 / 4.57 ( 2541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.391 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0446 time to fit residues: 6.0127 Evaluate side-chains 66 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 20.0000 chunk 196 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 chunk 166 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 overall best weight: 9.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.039995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.030663 restraints weight = 131821.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.030925 restraints weight = 114492.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.031288 restraints weight = 103907.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.031566 restraints weight = 94108.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.031828 restraints weight = 85257.792| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.9463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10608 Z= 0.399 Angle : 0.643 4.718 14790 Z= 0.432 Chirality : 0.044 0.153 1992 Planarity : 0.004 0.013 2112 Dihedral : 7.274 70.955 2124 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2100 helix: -0.06 (0.16), residues: 1002 sheet: -2.59 (0.27), residues: 330 loop : -1.28 (0.22), residues: 768 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/Z covalent geometry : bond 0.00592 / 0.40 (10608) covalent geometry : angle 0.64289 / 0.43 (14790) hydrogen bonds : bond 0.05654 / 4.35 ( 877) hydrogen bonds : angle 7.18178 / 5.56 ( 2541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1372.30 seconds wall clock time: 24 minutes 8.88 seconds (1448.88 seconds total)