Starting phenix.real_space_refine on Thu Mar 5 04:29:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6olm_20117/03_2026/6olm_20117.cif Found real_map, /net/cci-nas-00/data/ceres_data/6olm_20117/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6olm_20117/03_2026/6olm_20117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6olm_20117/03_2026/6olm_20117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6olm_20117/03_2026/6olm_20117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6olm_20117/03_2026/6olm_20117.map" } 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-dev-5986/lib/python3.9/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: 1.42, per 1000 atoms: 0.13 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: 1.16 Conformation dependent library (CDL) restraints added in 758.9 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: 0.67 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: 1.90 Time building geometry restraints manager: 1.49 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: 6102 16.11 - 32.22: 42 32.22 - 48.33: 90 48.33 - 64.44: 6 64.44 - 80.54: 6 Dihedral angle restraints: 6246 sinusoidal: 204 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 6243 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: 0.04 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: 1.540 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 10.913 80.545 2310 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 covalent geometry : bond 0.01212 (10608) covalent geometry : angle 1.28068 (14790) hydrogen bonds : bond 0.14045 ( 877) hydrogen bonds : angle 7.45570 ( 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 : 0.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0468 time to fit residues: 6.1834 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 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.041995 restraints weight = 110999.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.042409 restraints weight = 98249.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.042773 restraints weight = 89556.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.043078 restraints weight = 82312.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.043328 restraints weight = 76815.203| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10608 Z= 0.246 Angle : 0.548 5.178 14790 Z= 0.351 Chirality : 0.044 0.136 1992 Planarity : 0.003 0.012 2112 Dihedral : 8.609 80.450 2310 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.00 % Favored : 97.71 % 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: 1.16 (0.19), residues: 2100 helix: 1.15 (0.17), residues: 1014 sheet: 1.10 (0.26), residues: 420 loop : 0.14 (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 covalent geometry : bond 0.00370 (10608) covalent geometry : angle 0.54844 (14790) hydrogen bonds : bond 0.05067 ( 877) hydrogen bonds : angle 5.45887 ( 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 : 0.397 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0412 time to fit residues: 5.5470 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 : 0.376 ------------------------------------------------------------------------------- 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: 30.0000 chunk 62 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 199 optimal weight: 40.0000 chunk 34 optimal weight: 2.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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 = 0.2969 r_free = 0.2969 target = 0.043763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.035850 restraints weight = 121141.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.036203 restraints weight = 104534.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.036628 restraints weight = 93493.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.036951 restraints weight = 85220.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.037129 restraints weight = 78341.778| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10608 Z= 0.415 Angle : 0.764 6.298 14790 Z= 0.489 Chirality : 0.045 0.156 1992 Planarity : 0.005 0.019 2112 Dihedral : 10.213 75.562 2310 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: -0.98 (0.17), residues: 2100 helix: -0.53 (0.16), residues: 918 sheet: -0.31 (0.26), residues: 384 loop : -0.73 (0.20), residues: 798 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 0.00582 (10608) covalent geometry : angle 0.76439 (14790) hydrogen bonds : bond 0.06707 ( 877) hydrogen bonds : angle 7.14926 ( 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 : 0.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0445 time to fit residues: 5.9233 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 : 0.367 ------------------------------------------------------------------------------- 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: 7.9990 chunk 120 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 94 optimal weight: 0.0470 overall best weight: 5.0086 ------------------------------------------------------------------------------- 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 = 0.2977 r_free = 0.2977 target = 0.044490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036283 restraints weight = 120849.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.036683 restraints weight = 104113.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.037097 restraints weight = 93473.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.037419 restraints weight = 84596.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.037621 restraints weight = 77851.637| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10608 Z= 0.235 Angle : 0.489 3.762 14790 Z= 0.321 Chirality : 0.043 0.150 1992 Planarity : 0.003 0.009 2112 Dihedral : 9.723 73.924 2310 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -0.31 (0.18), residues: 2100 helix: 0.45 (0.16), residues: 1002 sheet: -0.87 (0.24), residues: 456 loop : -0.45 (0.24), residues: 642 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 0.00360 (10608) covalent geometry : angle 0.48943 (14790) hydrogen bonds : bond 0.04136 ( 877) hydrogen bonds : angle 6.02197 ( 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 : 0.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0425 time to fit residues: 5.7223 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 : 0.337 ------------------------------------------------------------------------------- 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: 0.7980 chunk 42 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 96 optimal weight: 40.0000 chunk 186 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 overall best weight: 4.9586 ------------------------------------------------------------------------------- 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 = 0.2949 r_free = 0.2949 target = 0.043009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.035175 restraints weight = 122033.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.035553 restraints weight = 107283.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.035869 restraints weight = 96623.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.036098 restraints weight = 88708.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.036341 restraints weight = 82939.933| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10608 Z= 0.247 Angle : 0.498 3.994 14790 Z= 0.321 Chirality : 0.043 0.143 1992 Planarity : 0.003 0.010 2112 Dihedral : 9.729 84.289 2310 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.19 (0.18), residues: 2100 helix: 0.84 (0.16), residues: 1026 sheet: -1.45 (0.27), residues: 360 loop : -0.64 (0.23), 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 0.00375 (10608) covalent geometry : angle 0.49784 (14790) hydrogen bonds : bond 0.03994 ( 877) hydrogen bonds : angle 5.88449 ( 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 : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0431 time to fit residues: 5.6931 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 : 0.343 ------------------------------------------------------------------------------- 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: 0.0570 chunk 200 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 chunk 109 optimal weight: 10.0000 chunk 24 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 196 optimal weight: 0.8980 overall best weight: 2.7982 ------------------------------------------------------------------------------- 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 = 0.2969 r_free = 0.2969 target = 0.043746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.035621 restraints weight = 119716.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.035934 restraints weight = 105570.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036311 restraints weight = 96091.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.036571 restraints weight = 88193.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.036751 restraints weight = 82219.563| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10608 Z= 0.142 Angle : 0.398 3.706 14790 Z= 0.256 Chirality : 0.042 0.141 1992 Planarity : 0.002 0.008 2112 Dihedral : 9.621 89.291 2310 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.19), residues: 2100 helix: 1.54 (0.17), residues: 1032 sheet: -1.37 (0.25), residues: 432 loop : -0.32 (0.26), 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 covalent geometry : bond 0.00220 (10608) covalent geometry : angle 0.39750 (14790) hydrogen bonds : bond 0.02829 ( 877) hydrogen bonds : angle 5.37500 ( 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 : 0.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0423 time to fit residues: 5.7169 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 : 0.345 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 156 optimal weight: 40.0000 chunk 206 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 overall best weight: 7.3994 ------------------------------------------------------------------------------- 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 = 0.2913 r_free = 0.2913 target = 0.041994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.034485 restraints weight = 122845.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.034852 restraints weight = 107931.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.035167 restraints weight = 97409.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.035352 restraints weight = 89046.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.035618 restraints weight = 83439.559| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10608 Z= 0.318 Angle : 0.564 4.021 14790 Z= 0.375 Chirality : 0.044 0.148 1992 Planarity : 0.004 0.012 2112 Dihedral : 9.846 87.151 2310 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % 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: -0.67 (0.18), residues: 2100 helix: 0.48 (0.16), residues: 1014 sheet: -1.74 (0.27), residues: 360 loop : -0.88 (0.23), residues: 726 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 0.00479 (10608) covalent geometry : angle 0.56353 (14790) hydrogen bonds : bond 0.04764 ( 877) hydrogen bonds : angle 6.44912 ( 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 : 0.390 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0418 time to fit residues: 5.6168 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 : 0.344 ------------------------------------------------------------------------------- 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: 30.0000 chunk 152 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 overall best weight: 11.1994 ------------------------------------------------------------------------------- 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 = 0.2783 r_free = 0.2783 target = 0.039727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.030322 restraints weight = 143231.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.030474 restraints weight = 132938.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.030706 restraints weight = 125481.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.030881 restraints weight = 115946.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.030958 restraints weight = 111562.634| |-----------------------------------------------------------------------------| r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.9262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 10608 Z= 0.483 Angle : 0.773 5.985 14790 Z= 0.514 Chirality : 0.045 0.157 1992 Planarity : 0.005 0.021 2112 Dihedral : 10.631 74.093 2310 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % 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: -2.29 (0.18), residues: 2100 helix: -1.06 (0.16), residues: 906 sheet: -2.61 (0.27), residues: 330 loop : -1.33 (0.22), residues: 864 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 0.00717 (10608) covalent geometry : angle 0.77263 (14790) hydrogen bonds : bond 0.06628 ( 877) hydrogen bonds : angle 8.38970 ( 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 : 0.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0393 time to fit residues: 5.2764 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 : 0.345 ------------------------------------------------------------------------------- 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: 4.9990 chunk 175 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 137 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.040723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.031084 restraints weight = 128344.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.031399 restraints weight = 111899.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.031728 restraints weight = 100849.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.031957 restraints weight = 92620.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.032100 restraints weight = 86463.127| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.9103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10608 Z= 0.235 Angle : 0.501 4.110 14790 Z= 0.328 Chirality : 0.043 0.148 1992 Planarity : 0.003 0.010 2112 Dihedral : 9.919 69.359 2310 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % 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: -1.54 (0.18), residues: 2100 helix: -0.01 (0.16), residues: 1008 sheet: -2.69 (0.26), residues: 330 loop : -1.42 (0.22), residues: 762 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 0.00356 (10608) covalent geometry : angle 0.50124 (14790) hydrogen bonds : bond 0.04106 ( 877) hydrogen bonds : angle 6.82577 ( 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 : 0.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0384 time to fit residues: 5.2100 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 : 0.347 ------------------------------------------------------------------------------- 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: 8.9990 chunk 127 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 21.9990 chunk 154 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 104 optimal weight: 30.0000 chunk 181 optimal weight: 0.9980 chunk 166 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.2814 r_free = 0.2814 target = 0.040087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.030733 restraints weight = 130473.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.031075 restraints weight = 112686.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.031422 restraints weight = 99873.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.031677 restraints weight = 91337.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.031833 restraints weight = 84731.780| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.9472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10608 Z= 0.341 Angle : 0.593 4.168 14790 Z= 0.393 Chirality : 0.044 0.148 1992 Planarity : 0.003 0.011 2112 Dihedral : 10.084 65.743 2310 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % 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: -1.92 (0.18), residues: 2100 helix: -0.34 (0.16), residues: 1008 sheet: -2.67 (0.23), residues: 414 loop : -1.46 (0.24), residues: 678 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 0.00512 (10608) covalent geometry : angle 0.59278 (14790) hydrogen bonds : bond 0.04968 ( 877) hydrogen bonds : angle 7.28478 ( 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 : 0.362 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0393 time to fit residues: 5.3600 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 : 0.332 ------------------------------------------------------------------------------- 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: 9.9990 chunk 196 optimal weight: 0.9990 chunk 22 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 94 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 27 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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 = 0.2817 r_free = 0.2817 target = 0.040221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.030794 restraints weight = 129963.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.031122 restraints weight = 112238.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.031416 restraints weight = 100026.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.031715 restraints weight = 90952.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.031869 restraints weight = 84617.074| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.9732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10608 Z= 0.308 Angle : 0.558 3.960 14790 Z= 0.370 Chirality : 0.043 0.149 1992 Planarity : 0.003 0.011 2112 Dihedral : 9.958 63.298 2310 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % 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: -1.89 (0.18), residues: 2100 helix: -0.25 (0.16), residues: 1014 sheet: -2.63 (0.23), residues: 402 loop : -1.65 (0.24), 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 0.00463 (10608) covalent geometry : angle 0.55789 (14790) hydrogen bonds : bond 0.04645 ( 877) hydrogen bonds : angle 7.12565 ( 2541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1212.58 seconds wall clock time: 21 minutes 46.03 seconds (1306.03 seconds total)