Starting phenix.real_space_refine (version: dev) on Tue Feb 21 23:54:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eki_31168/02_2023/7eki_31168_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eki_31168/02_2023/7eki_31168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eki_31168/02_2023/7eki_31168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eki_31168/02_2023/7eki_31168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eki_31168/02_2023/7eki_31168_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eki_31168/02_2023/7eki_31168_updated.pdb" } resolution = 3.18 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= 0.010 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16005 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 3200 Chain: "B" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 3200 Chain: "C" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 3200 Chain: "D" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 3200 Chain: "E" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 3200 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.98, per 1000 atoms: 1.00 Number of scatterers: 16005 At special positions: 0 Unit cell: (92.92, 93.93, 164.63, 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) S 115 16.00 O 2855 8.00 N 2555 7.00 C 10480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 46 " " NAG B 601 " - " ASN B 46 " " NAG C 601 " - " ASN C 46 " " NAG D 601 " - " ASN D 46 " " NAG E 601 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 4.1 seconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 25 sheets defined 39.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.912A pdb=" N LYS A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.873A pdb=" N LEU A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 280 removed outlier: 3.736A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.640A pdb=" N VAL A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.925A pdb=" N ILE A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 433 through 489 removed outlier: 3.536A pdb=" N TYR A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'B' and resid 24 through 33 removed outlier: 3.912A pdb=" N LYS B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.873A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.736A pdb=" N THR B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 318 removed outlier: 3.640A pdb=" N VAL B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.926A pdb=" N ILE B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 433 through 489 removed outlier: 3.537A pdb=" N TYR B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 461 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'C' and resid 24 through 33 removed outlier: 3.911A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.873A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 280 removed outlier: 3.736A pdb=" N THR C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU C 278 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 318 removed outlier: 3.639A pdb=" N VAL C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.925A pdb=" N ILE C 334 " --> pdb=" O TRP C 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'C' and resid 433 through 489 removed outlier: 3.536A pdb=" N TYR C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 461 " --> pdb=" O CYS C 457 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 Processing helix chain 'D' and resid 24 through 33 removed outlier: 3.911A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 238 through 253 removed outlier: 3.873A pdb=" N LEU D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 280 removed outlier: 3.737A pdb=" N THR D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 277 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU D 278 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 318 removed outlier: 3.640A pdb=" N VAL D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 335 removed outlier: 3.925A pdb=" N ILE D 334 " --> pdb=" O TRP D 330 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 335 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 342 No H-bonds generated for 'chain 'D' and resid 339 through 342' Processing helix chain 'D' and resid 433 through 489 removed outlier: 3.537A pdb=" N TYR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 461 " --> pdb=" O CYS D 457 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.911A pdb=" N LYS E 28 " --> pdb=" O GLU E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 238 through 253 removed outlier: 3.873A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 280 removed outlier: 3.736A pdb=" N THR E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU E 277 " --> pdb=" O THR E 273 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU E 278 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 318 removed outlier: 3.640A pdb=" N VAL E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 removed outlier: 3.925A pdb=" N ILE E 334 " --> pdb=" O TRP E 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 335 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 342 No H-bonds generated for 'chain 'E' and resid 339 through 342' Processing helix chain 'E' and resid 433 through 489 removed outlier: 3.537A pdb=" N TYR E 442 " --> pdb=" O GLU E 438 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 461 " --> pdb=" O CYS E 457 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 487 " --> pdb=" O THR E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 499 Processing sheet with id= A, first strand: chain 'A' and resid 178 through 182 removed outlier: 6.127A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 53 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 79 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN A 75 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 64 through 66 Processing sheet with id= C, first strand: chain 'A' and resid 80 through 83 Processing sheet with id= D, first strand: chain 'A' and resid 100 through 102 Processing sheet with id= E, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 208 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG A 227 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A 198 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 178 through 182 removed outlier: 6.127A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 79 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN B 75 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR B 73 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 64 through 66 Processing sheet with id= H, first strand: chain 'B' and resid 80 through 83 Processing sheet with id= I, first strand: chain 'B' and resid 100 through 102 Processing sheet with id= J, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.527A pdb=" N GLY B 169 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 208 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG B 227 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU B 198 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.127A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 79 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 64 through 66 Processing sheet with id= M, first strand: chain 'C' and resid 80 through 83 Processing sheet with id= N, first strand: chain 'C' and resid 100 through 102 Processing sheet with id= O, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY C 169 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 208 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG C 227 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU C 198 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 178 through 182 removed outlier: 6.128A pdb=" N LEU D 51 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLN D 181 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 53 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D 79 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN D 75 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 64 through 66 Processing sheet with id= R, first strand: chain 'D' and resid 80 through 83 Processing sheet with id= S, first strand: chain 'D' and resid 100 through 102 Processing sheet with id= T, first strand: chain 'D' and resid 112 through 114 removed outlier: 3.527A pdb=" N GLY D 169 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 208 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG D 227 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU D 198 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 178 through 182 removed outlier: 6.127A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN E 79 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN E 75 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= W, first strand: chain 'E' and resid 80 through 83 Processing sheet with id= X, first strand: chain 'E' and resid 100 through 102 Processing sheet with id= Y, first strand: chain 'E' and resid 112 through 114 removed outlier: 3.526A pdb=" N GLY E 169 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 208 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG E 227 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU E 198 " --> pdb=" O ARG E 227 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1995 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: 4.85 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4890 1.35 - 1.47: 4220 1.47 - 1.59: 7155 1.59 - 1.71: 20 1.71 - 1.83: 170 Bond restraints: 16455 Sorted by residual: bond pdb=" C3 CLR E 602 " pdb=" O1 CLR E 602 " ideal model delta sigma weight residual 1.413 1.511 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C3 CLR B 602 " pdb=" O1 CLR B 602 " ideal model delta sigma weight residual 1.413 1.510 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3 CLR C 602 " pdb=" O1 CLR C 602 " ideal model delta sigma weight residual 1.413 1.510 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3 CLR D 602 " pdb=" O1 CLR D 602 " ideal model delta sigma weight residual 1.413 1.510 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3 CLR A 602 " pdb=" O1 CLR A 602 " ideal model delta sigma weight residual 1.413 1.510 -0.097 2.00e-02 2.50e+03 2.33e+01 ... (remaining 16450 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.12: 613 107.12 - 113.86: 9436 113.86 - 120.60: 6469 120.60 - 127.35: 5759 127.35 - 134.09: 213 Bond angle restraints: 22490 Sorted by residual: angle pdb=" CB GLU B 452 " pdb=" CG GLU B 452 " pdb=" CD GLU B 452 " ideal model delta sigma weight residual 112.60 120.00 -7.40 1.70e+00 3.46e-01 1.89e+01 angle pdb=" CB GLU E 452 " pdb=" CG GLU E 452 " pdb=" CD GLU E 452 " ideal model delta sigma weight residual 112.60 119.98 -7.38 1.70e+00 3.46e-01 1.88e+01 angle pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " pdb=" CD GLU A 452 " ideal model delta sigma weight residual 112.60 119.97 -7.37 1.70e+00 3.46e-01 1.88e+01 angle pdb=" CB GLU C 452 " pdb=" CG GLU C 452 " pdb=" CD GLU C 452 " ideal model delta sigma weight residual 112.60 119.96 -7.36 1.70e+00 3.46e-01 1.88e+01 angle pdb=" CB GLU D 452 " pdb=" CG GLU D 452 " pdb=" CD GLU D 452 " ideal model delta sigma weight residual 112.60 119.95 -7.35 1.70e+00 3.46e-01 1.87e+01 ... (remaining 22485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 8733 15.88 - 31.76: 662 31.76 - 47.65: 185 47.65 - 63.53: 15 63.53 - 79.41: 10 Dihedral angle restraints: 9605 sinusoidal: 3775 harmonic: 5830 Sorted by residual: dihedral pdb=" CA CYS C 212 " pdb=" C CYS C 212 " pdb=" N CYS C 213 " pdb=" CA CYS C 213 " ideal model delta harmonic sigma weight residual 180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA CYS D 212 " pdb=" C CYS D 212 " pdb=" N CYS D 213 " pdb=" CA CYS D 213 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS E 212 " pdb=" C CYS E 212 " pdb=" N CYS E 213 " pdb=" CA CYS E 213 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 9602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2531 0.114 - 0.227: 64 0.227 - 0.341: 0 0.341 - 0.454: 10 0.454 - 0.568: 15 Chirality restraints: 2620 Sorted by residual: chirality pdb=" C3 CLR E 602 " pdb=" C2 CLR E 602 " pdb=" C4 CLR E 602 " pdb=" O1 CLR E 602 " both_signs ideal model delta sigma weight residual False -2.46 -3.02 0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" C14 CLR E 602 " pdb=" C13 CLR E 602 " pdb=" C15 CLR E 602 " pdb=" C8 CLR E 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.88 0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" C3 CLR D 602 " pdb=" C2 CLR D 602 " pdb=" C4 CLR D 602 " pdb=" O1 CLR D 602 " both_signs ideal model delta sigma weight residual False -2.46 -3.02 0.57 2.00e-01 2.50e+01 8.03e+00 ... (remaining 2617 not shown) Planarity restraints: 2765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 490 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO D 491 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 491 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 491 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 490 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO E 491 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 491 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 491 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 490 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 491 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.018 5.00e-02 4.00e+02 ... (remaining 2762 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2646 2.76 - 3.30: 14324 3.30 - 3.83: 24962 3.83 - 4.37: 28550 4.37 - 4.90: 51561 Nonbonded interactions: 122043 Sorted by model distance: nonbonded pdb=" OD1 ASP B 123 " pdb=" OG1 THR B 125 " model vdw 2.230 2.440 nonbonded pdb=" OD1 ASP A 123 " pdb=" OG1 THR A 125 " model vdw 2.230 2.440 nonbonded pdb=" OD1 ASP E 123 " pdb=" OG1 THR E 125 " model vdw 2.230 2.440 nonbonded pdb=" OD1 ASP D 123 " pdb=" OG1 THR D 125 " model vdw 2.230 2.440 nonbonded pdb=" OD1 ASP C 123 " pdb=" OG1 THR C 125 " model vdw 2.231 2.440 ... (remaining 122038 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' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 502 or resid 601 throu \ gh 602)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 S 115 5.16 5 C 10480 2.51 5 N 2555 2.21 5 O 2855 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.540 Check model and map are aligned: 0.220 Process input model: 50.520 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.005 0.098 16455 Z= 0.309 Angle : 0.608 9.959 22490 Z= 0.299 Chirality : 0.062 0.568 2620 Planarity : 0.003 0.033 2755 Dihedral : 12.253 79.410 5805 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.88 (0.18), residues: 1960 helix: -0.98 (0.18), residues: 760 sheet: -0.88 (0.23), residues: 445 loop : -1.56 (0.23), residues: 755 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 1.915 Fit side-chains outliers start: 15 outliers final: 1 residues processed: 209 average time/residue: 0.2835 time to fit residues: 89.0699 Evaluate side-chains 161 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1703 time to fit residues: 2.6407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 16455 Z= 0.322 Angle : 0.593 9.922 22490 Z= 0.309 Chirality : 0.044 0.156 2620 Planarity : 0.004 0.036 2755 Dihedral : 4.932 45.853 2270 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.41 (0.18), residues: 1960 helix: 0.05 (0.19), residues: 735 sheet: -0.79 (0.23), residues: 455 loop : -1.92 (0.21), residues: 770 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 26 residues processed: 188 average time/residue: 0.2897 time to fit residues: 81.4690 Evaluate side-chains 187 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1381 time to fit residues: 9.2824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 147 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 0.0060 chunk 191 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 175 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 142 optimal weight: 0.0020 overall best weight: 0.3204 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 16455 Z= 0.142 Angle : 0.490 9.106 22490 Z= 0.253 Chirality : 0.039 0.138 2620 Planarity : 0.003 0.037 2755 Dihedral : 4.625 40.704 2270 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.19), residues: 1960 helix: 0.81 (0.19), residues: 730 sheet: -0.40 (0.24), residues: 455 loop : -1.91 (0.21), residues: 775 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 178 average time/residue: 0.2884 time to fit residues: 76.5818 Evaluate side-chains 166 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1537 time to fit residues: 3.1881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 16455 Z= 0.313 Angle : 0.561 9.282 22490 Z= 0.289 Chirality : 0.043 0.159 2620 Planarity : 0.004 0.037 2755 Dihedral : 4.739 33.908 2270 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.19), residues: 1960 helix: 0.77 (0.19), residues: 755 sheet: -0.55 (0.24), residues: 445 loop : -2.01 (0.21), residues: 760 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 188 average time/residue: 0.2914 time to fit residues: 81.8615 Evaluate side-chains 197 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1533 time to fit residues: 7.3217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.0980 chunk 169 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 16455 Z= 0.149 Angle : 0.480 8.724 22490 Z= 0.246 Chirality : 0.039 0.140 2620 Planarity : 0.003 0.035 2755 Dihedral : 4.574 32.467 2270 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.19), residues: 1960 helix: 0.91 (0.19), residues: 760 sheet: -0.30 (0.24), residues: 445 loop : -1.91 (0.22), residues: 755 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 182 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 183 average time/residue: 0.2903 time to fit residues: 79.2521 Evaluate side-chains 169 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1424 time to fit residues: 2.8249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 16455 Z= 0.334 Angle : 0.565 9.105 22490 Z= 0.289 Chirality : 0.043 0.160 2620 Planarity : 0.004 0.036 2755 Dihedral : 4.726 29.232 2270 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.19), residues: 1960 helix: 0.75 (0.18), residues: 780 sheet: -0.40 (0.24), residues: 445 loop : -2.07 (0.22), residues: 735 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 187 average time/residue: 0.2856 time to fit residues: 80.0515 Evaluate side-chains 197 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1411 time to fit residues: 6.4630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 16455 Z= 0.152 Angle : 0.491 8.844 22490 Z= 0.249 Chirality : 0.039 0.143 2620 Planarity : 0.003 0.035 2755 Dihedral : 4.580 29.960 2270 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.19), residues: 1960 helix: 0.92 (0.18), residues: 780 sheet: -0.24 (0.24), residues: 445 loop : -2.04 (0.22), residues: 735 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 173 average time/residue: 0.2974 time to fit residues: 76.6659 Evaluate side-chains 169 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1406 time to fit residues: 2.9125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 119 optimal weight: 0.0270 chunk 128 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 147 optimal weight: 0.0020 chunk 170 optimal weight: 5.9990 overall best weight: 1.2648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16455 Z= 0.192 Angle : 0.507 8.452 22490 Z= 0.255 Chirality : 0.040 0.134 2620 Planarity : 0.003 0.036 2755 Dihedral : 4.528 28.857 2270 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.19), residues: 1960 helix: 0.91 (0.18), residues: 780 sheet: -0.24 (0.24), residues: 445 loop : -2.03 (0.22), residues: 735 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 171 average time/residue: 0.2953 time to fit residues: 75.1065 Evaluate side-chains 167 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.842 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1587 time to fit residues: 3.2105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16455 Z= 0.154 Angle : 0.486 8.262 22490 Z= 0.244 Chirality : 0.039 0.136 2620 Planarity : 0.003 0.035 2755 Dihedral : 4.447 28.961 2270 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.19), residues: 1960 helix: 0.99 (0.18), residues: 780 sheet: -0.17 (0.25), residues: 445 loop : -2.08 (0.22), residues: 735 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.3048 time to fit residues: 76.3348 Evaluate side-chains 163 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 128 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 16455 Z= 0.227 Angle : 0.523 8.705 22490 Z= 0.263 Chirality : 0.040 0.137 2620 Planarity : 0.003 0.036 2755 Dihedral : 4.491 27.531 2270 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.19), residues: 1960 helix: 0.92 (0.18), residues: 785 sheet: -0.23 (0.25), residues: 445 loop : -2.11 (0.22), residues: 730 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.3020 time to fit residues: 76.3518 Evaluate side-chains 165 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.861 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 142 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 136 optimal weight: 0.0470 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103040 restraints weight = 35243.125| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.09 r_work: 0.3100 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 16455 Z= 0.142 Angle : 0.483 8.624 22490 Z= 0.243 Chirality : 0.038 0.139 2620 Planarity : 0.003 0.034 2755 Dihedral : 4.376 27.931 2270 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.19), residues: 1960 helix: 1.03 (0.18), residues: 790 sheet: -0.15 (0.25), residues: 455 loop : -2.08 (0.22), residues: 715 =============================================================================== Job complete usr+sys time: 2959.42 seconds wall clock time: 54 minutes 27.56 seconds (3267.56 seconds total)