Starting phenix.real_space_refine on Mon Mar 18 14:44:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/03_2024/6olm_20117_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/03_2024/6olm_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_20117/03_2024/6olm_20117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/03_2024/6olm_20117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/03_2024/6olm_20117_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olm_20117/03_2024/6olm_20117_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.53, per 1000 atoms: 0.71 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: 5.67 Conformation dependent library (CDL) restraints added in 2.8 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: 2.82 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: 3.67 Time building geometry restraints manager: 4.81 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: 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: 2.40 - 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 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 4.140 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.530 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.770 ------------------------------------------------------------------------------- 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= 0.909 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 : 2.397 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 1.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0952 time to fit residues: 13.2166 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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: 3.9990 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: 3.9986 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.2414 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= 0.243 Angle : 0.519 3.990 14790 Z= 0.332 Chirality : 0.045 0.127 1992 Planarity : 0.003 0.011 2112 Dihedral : 8.092 87.224 2310 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.29 % Favored : 98.43 % 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 (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: 1.20 (0.18), residues: 2100 helix: 1.34 (0.17), residues: 930 sheet: 1.04 (0.26), residues: 432 loop : 0.07 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 1.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0914 time to fit residues: 12.8369 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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: 0.9980 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: 8.9990 chunk 189 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- 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: 0.8292 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10608 Z= 0.372 Angle : 0.650 4.301 14790 Z= 0.422 Chirality : 0.044 0.149 1992 Planarity : 0.004 0.013 2112 Dihedral : 9.441 77.465 2310 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 (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: -0.45 (0.17), residues: 2100 helix: 0.15 (0.16), residues: 894 sheet: -0.08 (0.26), residues: 390 loop : -0.74 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 1.161 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0955 time to fit residues: 13.2730 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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: 0.9980 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 0.0270 chunk 191 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 overall best weight: 2.5842 ------------------------------------------------------------------------------- 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: 0.8250 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10608 Z= 0.146 Angle : 0.383 3.256 14790 Z= 0.252 Chirality : 0.043 0.142 1992 Planarity : 0.002 0.009 2112 Dihedral : 8.758 78.020 2310 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 2100 helix: 1.72 (0.17), residues: 930 sheet: -0.32 (0.24), residues: 456 loop : 0.29 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 1.153 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0983 time to fit residues: 13.7873 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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: 0.3980 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 7.0788 ------------------------------------------------------------------------------- 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: 0.8329 moved from start: 0.6894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10608 Z= 0.358 Angle : 0.585 4.154 14790 Z= 0.386 Chirality : 0.043 0.143 1992 Planarity : 0.004 0.013 2112 Dihedral : 9.341 76.633 2310 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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 (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: -0.17 (0.18), residues: 2100 helix: 0.86 (0.16), residues: 900 sheet: -1.03 (0.25), residues: 444 loop : -0.53 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 1.154 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0938 time to fit residues: 13.0274 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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: 8.9990 chunk 182 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 40.0000 chunk 67 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10608 Z= 0.342 Angle : 0.580 4.418 14790 Z= 0.384 Chirality : 0.043 0.144 1992 Planarity : 0.004 0.014 2112 Dihedral : 9.950 74.349 2310 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % 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 (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: -1.08 (0.18), residues: 2100 helix: -0.07 (0.16), residues: 882 sheet: -1.51 (0.26), residues: 414 loop : -0.77 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 0.949 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0967 time to fit residues: 13.3576 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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: 0.2980 chunk 148 optimal weight: 50.0000 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 overall best weight: 8.0590 ------------------------------------------------------------------------------- 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: 0.8381 moved from start: 0.8595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10608 Z= 0.377 Angle : 0.607 4.407 14790 Z= 0.401 Chirality : 0.044 0.149 1992 Planarity : 0.004 0.013 2112 Dihedral : 10.308 71.095 2310 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % 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 (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: -1.57 (0.18), residues: 2100 helix: -0.47 (0.16), residues: 882 sheet: -1.90 (0.26), residues: 414 loop : -0.95 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 1.320 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0976 time to fit residues: 13.5703 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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: 0.7980 chunk 120 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 18 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 184 optimal weight: 20.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- 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: 0.8361 moved from start: 0.8590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10608 Z= 0.234 Angle : 0.473 3.054 14790 Z= 0.313 Chirality : 0.043 0.145 1992 Planarity : 0.003 0.010 2112 Dihedral : 10.012 70.441 2310 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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 (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: -0.98 (0.18), residues: 2100 helix: 0.20 (0.16), residues: 906 sheet: -1.81 (0.26), residues: 402 loop : -0.80 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 1.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0956 time to fit residues: 13.4578 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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: 5.9990 chunk 176 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 113 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 148 optimal weight: 50.0000 chunk 57 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.9009 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= 0.326 Angle : 0.553 3.970 14790 Z= 0.365 Chirality : 0.043 0.148 1992 Planarity : 0.003 0.011 2112 Dihedral : 10.356 71.514 2310 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % 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 (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: -1.37 (0.18), residues: 2100 helix: -0.09 (0.16), residues: 894 sheet: -2.16 (0.25), residues: 414 loop : -0.91 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** 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 : 1.163 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0946 time to fit residues: 13.3537 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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: 20.0000 chunk 121 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 30.0000 chunk 192 optimal weight: 50.0000 chunk 166 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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: 0.8392 moved from start: 0.9422 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= 0.343 Angle : 0.572 4.174 14790 Z= 0.379 Chirality : 0.043 0.146 1992 Planarity : 0.003 0.012 2112 Dihedral : 10.579 77.610 2310 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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 (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: -1.74 (0.18), residues: 2100 helix: -0.50 (0.16), residues: 894 sheet: -2.13 (0.24), residues: 396 loop : -1.15 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 ********************** 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 : 1.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0984 time to fit residues: 13.6547 Evaluate side-chains 66 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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: 0.0470 chunk 153 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 30.0000 chunk 146 optimal weight: 6.9990 overall best weight: 3.1684 ------------------------------------------------------------------------------- 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 = 0.2857 r_free = 0.2857 target = 0.042412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.032305 restraints weight = 137132.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.032486 restraints weight = 128257.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.032646 restraints weight = 121201.091| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.9250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10608 Z= 0.157 Angle : 0.411 2.899 14790 Z= 0.271 Chirality : 0.043 0.136 1992 Planarity : 0.002 0.010 2112 Dihedral : 9.985 74.756 2310 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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 (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: -0.76 (0.19), residues: 2100 helix: 0.70 (0.17), residues: 918 sheet: -2.13 (0.24), residues: 396 loop : -0.88 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1418.21 seconds wall clock time: 29 minutes 24.94 seconds (1764.94 seconds total)