Starting phenix.real_space_refine (version: dev) on Wed Dec 14 15:27:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/12_2022/6olm_20117_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/12_2022/6olm_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/12_2022/6olm_20117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/12_2022/6olm_20117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/12_2022/6olm_20117_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/12_2022/6olm_20117_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 12 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: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "B" Number of atoms: 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: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "C" Number of atoms: 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: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "D" Number of atoms: 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: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "E" Number of atoms: 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: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "F" Number of atoms: 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: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.29, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 2.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 96 helices and 12 sheets defined 43.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.137A pdb=" N ILE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.641A pdb=" N GLU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 186 through 196 removed outlier: 4.713A pdb=" N LEU A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 247 through 260 Proline residue: A 251 - end of helix Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.630A pdb=" N TYR A 304 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 45 through 55 removed outlier: 4.137A pdb=" N ILE B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 67 Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.642A pdb=" N GLU B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'B' and resid 186 through 196 removed outlier: 4.713A pdb=" N LEU B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 234 through 243 Processing helix chain 'B' and resid 247 through 260 Proline residue: B 251 - end of helix Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.629A pdb=" N TYR B 304 " --> pdb=" O HIS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 334 through 340 Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 45 through 55 removed outlier: 4.138A pdb=" N ILE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 107 through 110 No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 114 through 121 removed outlier: 3.642A pdb=" N GLU C 121 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 186 through 196 removed outlier: 4.713A pdb=" N LEU C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 196 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 247 through 260 Proline residue: C 251 - end of helix Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.629A pdb=" N TYR C 304 " --> pdb=" O HIS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 314 No H-bonds generated for 'chain 'C' and resid 311 through 314' Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 45 through 55 removed outlier: 4.138A pdb=" N ILE D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 67 Processing helix chain 'D' and resid 107 through 110 No H-bonds generated for 'chain 'D' and resid 107 through 110' Processing helix chain 'D' and resid 114 through 121 removed outlier: 3.642A pdb=" N GLU D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 151 Processing helix chain 'D' and resid 186 through 196 removed outlier: 4.713A pdb=" N LEU D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN D 196 " --> pdb=" O TYR D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 234 through 243 Processing helix chain 'D' and resid 247 through 260 Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.630A pdb=" N TYR D 304 " --> pdb=" O HIS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 314 No H-bonds generated for 'chain 'D' and resid 311 through 314' Processing helix chain 'D' and resid 319 through 328 Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'D' and resid 344 through 351 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 45 through 55 removed outlier: 4.137A pdb=" N ILE E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'E' and resid 107 through 110 No H-bonds generated for 'chain 'E' and resid 107 through 110' Processing helix chain 'E' and resid 114 through 121 removed outlier: 3.642A pdb=" N GLU E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 151 Processing helix chain 'E' and resid 186 through 196 removed outlier: 4.713A pdb=" N LEU E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'E' and resid 247 through 260 Proline residue: E 251 - end of helix Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 300 through 309 removed outlier: 3.629A pdb=" N TYR E 304 " --> pdb=" O HIS E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 314 No H-bonds generated for 'chain 'E' and resid 311 through 314' Processing helix chain 'E' and resid 319 through 328 Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 344 through 351 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 45 through 55 removed outlier: 4.138A pdb=" N ILE F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 67 Processing helix chain 'F' and resid 107 through 110 No H-bonds generated for 'chain 'F' and resid 107 through 110' Processing helix chain 'F' and resid 114 through 121 removed outlier: 3.642A pdb=" N GLU F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 151 Processing helix chain 'F' and resid 186 through 196 removed outlier: 4.712A pdb=" N LEU F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN F 196 " --> pdb=" O TYR F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 234 through 243 Processing helix chain 'F' and resid 247 through 260 Proline residue: F 251 - end of helix Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 300 through 309 removed outlier: 3.629A pdb=" N TYR F 304 " --> pdb=" O HIS F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 314 No H-bonds generated for 'chain 'F' and resid 311 through 314' Processing helix chain 'F' and resid 319 through 328 Processing helix chain 'F' and resid 334 through 340 Processing helix chain 'F' and resid 344 through 351 Processing sheet with id= A, first strand: chain 'A' and resid 69 through 76 Processing sheet with id= B, first strand: chain 'A' and resid 173 through 178 removed outlier: 6.412A pdb=" N VAL A 200 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 159 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 202 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 224 " --> pdb=" O VAL A 201 " (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: 6.900A pdb=" N LEU A 128 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 264 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR A 130 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 266 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 69 through 76 Processing sheet with id= D, first strand: chain 'B' and resid 173 through 178 removed outlier: 6.412A pdb=" N VAL B 200 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL B 159 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 202 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 224 " --> pdb=" O VAL B 201 " (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: 6.899A pdb=" N LEU B 128 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 264 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR B 130 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER B 266 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 69 through 76 Processing sheet with id= F, first strand: chain 'C' and resid 173 through 178 removed outlier: 6.412A pdb=" N VAL C 200 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL C 159 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU C 202 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 224 " --> pdb=" O VAL C 201 " (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: 6.900A pdb=" N LEU C 128 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 264 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR C 130 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER C 266 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 69 through 76 Processing sheet with id= H, first strand: chain 'D' and resid 173 through 178 removed outlier: 6.412A pdb=" N VAL D 200 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL D 159 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU D 202 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU D 224 " --> pdb=" O VAL D 201 " (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: 6.899A pdb=" N LEU D 128 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D 264 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR D 130 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER D 266 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 69 through 76 Processing sheet with id= J, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.412A pdb=" N VAL E 200 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL E 159 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU E 202 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU E 224 " --> pdb=" O VAL E 201 " (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: 6.899A pdb=" N LEU E 128 " --> pdb=" O GLU E 262 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL E 264 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR E 130 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER E 266 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 69 through 76 Processing sheet with id= L, first strand: chain 'F' and resid 173 through 178 removed outlier: 6.413A pdb=" N VAL F 200 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL F 159 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU F 202 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU F 224 " --> pdb=" O VAL F 201 " (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: 6.900A pdb=" N LEU F 128 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL F 264 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR F 130 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER F 266 " --> pdb=" O THR F 130 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 5.59 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: 101.22 - 107.42: 383 107.42 - 113.63: 5750 113.63 - 119.83: 3079 119.83 - 126.03: 5536 126.03 - 132.23: 42 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: 2.40 - 2.90: 4713 2.90 - 3.40: 10798 3.40 - 3.90: 15361 3.90 - 4.40: 16488 4.40 - 4.90: 26128 Nonbonded interactions: 73488 Sorted by model distance: nonbonded pdb=" O PHE D 64 " pdb=" N ASN D 68 " model vdw 2.397 2.520 nonbonded pdb=" O PHE A 64 " pdb=" N ASN A 68 " model vdw 2.398 2.520 nonbonded pdb=" O PHE E 64 " pdb=" N ASN E 68 " model vdw 2.398 2.520 nonbonded pdb=" O PHE F 64 " pdb=" N ASN F 68 " model vdw 2.398 2.520 nonbonded pdb=" O PHE C 64 " pdb=" N ASN C 68 " model vdw 2.398 2.520 ... (remaining 73483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 4.580 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 35.040 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- 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= 0.909 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 : 2.397 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1048 time to fit residues: 14.9559 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 20.0000 chunk 159 optimal weight: 0.0670 chunk 88 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 164 optimal weight: 50.0000 chunk 63 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 40.0000 chunk 190 optimal weight: 9.9990 overall best weight: 3.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10608 Z= 0.189 Angle : 0.486 4.737 14790 Z= 0.304 Chirality : 0.044 0.131 1992 Planarity : 0.003 0.009 2112 Dihedral : 6.021 74.544 2124 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.14 % Favored : 98.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 2100 helix: 1.47 (0.17), residues: 978 sheet: 1.22 (0.26), residues: 420 loop : -0.03 (0.22), residues: 702 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0980 time to fit residues: 13.9603 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 158 optimal weight: 20.0000 chunk 129 optimal weight: 50.0000 chunk 52 optimal weight: 30.0000 chunk 191 optimal weight: 30.0000 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 0.5980 chunk 189 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 overall best weight: 12.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.117 10608 Z= 0.642 Angle : 0.917 9.856 14790 Z= 0.593 Chirality : 0.047 0.159 1992 Planarity : 0.006 0.027 2112 Dihedral : 7.550 31.048 2124 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2100 helix: -1.70 (0.14), residues: 840 sheet: -0.40 (0.25), residues: 444 loop : -1.01 (0.20), residues: 816 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0981 time to fit residues: 13.7092 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 191 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 100 optimal weight: 0.0870 chunk 181 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 overall best weight: 4.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10608 Z= 0.222 Angle : 0.466 2.970 14790 Z= 0.305 Chirality : 0.043 0.142 1992 Planarity : 0.003 0.008 2112 Dihedral : 6.152 35.922 2124 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2100 helix: 0.21 (0.16), residues: 894 sheet: -0.90 (0.26), residues: 390 loop : -0.29 (0.21), residues: 816 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.426 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1090 time to fit residues: 15.3678 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.7087 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= 0.324 Angle : 0.545 4.234 14790 Z= 0.361 Chirality : 0.044 0.141 1992 Planarity : 0.003 0.011 2112 Dihedral : 6.269 29.079 2124 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2100 helix: 0.15 (0.16), residues: 888 sheet: -1.36 (0.26), residues: 420 loop : -0.49 (0.22), residues: 792 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.243 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0972 time to fit residues: 13.8350 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 203 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.8374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10608 Z= 0.316 Angle : 0.552 4.139 14790 Z= 0.365 Chirality : 0.044 0.147 1992 Planarity : 0.003 0.013 2112 Dihedral : 6.430 30.751 2124 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2100 helix: -0.15 (0.16), residues: 900 sheet: -1.73 (0.25), residues: 414 loop : -0.76 (0.24), residues: 786 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0967 time to fit residues: 13.6040 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 40.0000 chunk 114 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 chunk 202 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 overall best weight: 12.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.9227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.072 10608 Z= 0.541 Angle : 0.775 6.197 14790 Z= 0.514 Chirality : 0.045 0.159 1992 Planarity : 0.005 0.023 2112 Dihedral : 7.610 31.651 2124 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 33.36 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.62 % Favored : 88.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.17), residues: 2100 helix: -1.94 (0.15), residues: 864 sheet: -2.18 (0.25), residues: 414 loop : -1.40 (0.23), residues: 822 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0998 time to fit residues: 14.1777 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.9150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10608 Z= 0.309 Angle : 0.551 4.065 14790 Z= 0.364 Chirality : 0.043 0.145 1992 Planarity : 0.003 0.012 2112 Dihedral : 6.761 33.610 2124 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.18), residues: 2100 helix: -1.11 (0.15), residues: 888 sheet: -2.05 (0.25), residues: 402 loop : -1.16 (0.23), residues: 810 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.201 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0921 time to fit residues: 12.8239 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 113 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 148 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 chunk 170 optimal weight: 0.9980 chunk 178 optimal weight: 0.0020 chunk 187 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 overall best weight: 7.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.9476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 10608 Z= 0.337 Angle : 0.564 4.965 14790 Z= 0.370 Chirality : 0.043 0.146 1992 Planarity : 0.003 0.012 2112 Dihedral : 6.516 35.584 2124 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.18), residues: 2100 helix: -0.82 (0.16), residues: 894 sheet: -2.19 (0.24), residues: 396 loop : -1.34 (0.24), residues: 810 *********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.389 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0968 time to fit residues: 13.6848 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 40.0000 chunk 121 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 30.0000 chunk 192 optimal weight: 50.0000 chunk 166 optimal weight: 30.0000 chunk 17 optimal weight: 50.0000 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.9859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 10608 Z= 0.393 Angle : 0.620 4.957 14790 Z= 0.410 Chirality : 0.044 0.150 1992 Planarity : 0.004 0.014 2112 Dihedral : 6.982 37.618 2124 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.18), residues: 2100 helix: -1.29 (0.15), residues: 882 sheet: -2.50 (0.23), residues: 402 loop : -1.51 (0.23), residues: 816 ********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0977 time to fit residues: 13.9177 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 30.0000 chunk 51 optimal weight: 0.0980 chunk 153 optimal weight: 0.4980 chunk 24 optimal weight: 0.0670 chunk 46 optimal weight: 6.9990 chunk 166 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 overall best weight: 1.6920 ------------------------------------------------------------------------------- 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 = 0.042256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034816 restraints weight = 119923.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.035137 restraints weight = 104424.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.035422 restraints weight = 94671.127| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.9468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 10608 Z= 0.124 Angle : 0.388 2.719 14790 Z= 0.252 Chirality : 0.043 0.143 1992 Planarity : 0.002 0.010 2112 Dihedral : 5.444 38.288 2124 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2100 helix: 0.74 (0.16), residues: 954 sheet: -2.16 (0.24), residues: 396 loop : -1.36 (0.23), residues: 750 =============================================================================== Job complete usr+sys time: 1353.33 seconds wall clock time: 25 minutes 26.92 seconds (1526.92 seconds total)