Starting phenix.real_space_refine on Sat Dec 9 16:13:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh5_10194/12_2023/6sh5_10194.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh5_10194/12_2023/6sh5_10194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh5_10194/12_2023/6sh5_10194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh5_10194/12_2023/6sh5_10194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh5_10194/12_2023/6sh5_10194.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh5_10194/12_2023/6sh5_10194.pdb" } resolution = 4.6 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= 0.000 sd= 0.003 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 Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6853 2.51 5 N 2338 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11529 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1647 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 16, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 556 Chain: "B" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1647 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 16, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 556 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1647 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 16, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 556 Chain: "D" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1647 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 16, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 556 Chain: "E" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1647 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 16, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 556 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1647 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 16, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 556 Chain: "G" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1647 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 16, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 556 Time building chain proxies: 7.75, per 1000 atoms: 0.67 Number of scatterers: 11529 At special positions: 0 Unit cell: (150.378, 149.319, 86.838, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2338 8.00 N 2338 7.00 C 6853 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: 5.09 Conformation dependent library (CDL) restraints added in 3.2 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 21 sheets defined 42.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.691A pdb=" N ARG A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.708A pdb=" N LYS A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.692A pdb=" N ARG B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA B 324 " --> pdb=" O ILE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.524A pdb=" N GLU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.707A pdb=" N LYS B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.680A pdb=" N ILE C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 246 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.691A pdb=" N ARG C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.641A pdb=" N ASN C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 390 through 402 removed outlier: 3.524A pdb=" N GLU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER C 415 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.708A pdb=" N LYS C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 240 removed outlier: 3.680A pdb=" N ILE D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 246 Processing helix chain 'D' and resid 248 through 255 removed outlier: 3.691A pdb=" N ARG D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA D 324 " --> pdb=" O ILE D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU D 395 " --> pdb=" O PRO D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 434 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.707A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 246 Processing helix chain 'E' and resid 248 through 255 removed outlier: 3.692A pdb=" N ARG E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 284 Processing helix chain 'E' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA E 324 " --> pdb=" O ILE E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU E 395 " --> pdb=" O PRO E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 415 " --> pdb=" O LYS E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 434 Processing helix chain 'E' and resid 438 through 446 removed outlier: 3.708A pdb=" N LYS E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 449 No H-bonds generated for 'chain 'E' and resid 447 through 449' Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 248 through 255 removed outlier: 3.691A pdb=" N ARG F 255 " --> pdb=" O TRP F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 284 Processing helix chain 'F' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS F 305 " --> pdb=" O ASP F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 324 removed outlier: 3.720A pdb=" N ALA F 324 " --> pdb=" O ILE F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU F 395 " --> pdb=" O PRO F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 434 Processing helix chain 'F' and resid 438 through 446 removed outlier: 3.708A pdb=" N LYS F 444 " --> pdb=" O HIS F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 449 No H-bonds generated for 'chain 'F' and resid 447 through 449' Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP G 186 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU G 239 " --> pdb=" O LYS G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 246 Processing helix chain 'G' and resid 248 through 255 removed outlier: 3.690A pdb=" N ARG G 255 " --> pdb=" O TRP G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 284 Processing helix chain 'G' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN G 304 " --> pdb=" O ASP G 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS G 305 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA G 324 " --> pdb=" O ILE G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing helix chain 'G' and resid 342 through 351 Processing helix chain 'G' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU G 395 " --> pdb=" O PRO G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS G 409 " --> pdb=" O GLU G 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS G 410 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER G 415 " --> pdb=" O LYS G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 434 Processing helix chain 'G' and resid 438 through 446 removed outlier: 3.707A pdb=" N LYS G 444 " --> pdb=" O HIS G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 449 No H-bonds generated for 'chain 'G' and resid 447 through 449' Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE A 169 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 122 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A 206 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN A 292 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER A 208 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU A 319 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU A 291 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 359 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 262 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 382 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE B 169 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 122 Processing sheet with id=AA6, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.261A pdb=" N ILE B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR B 206 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN B 292 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER B 208 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU B 317 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 289 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU B 319 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU B 291 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 359 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 262 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 382 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE C 169 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 116 through 122 Processing sheet with id=AA9, first strand: chain 'C' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR C 206 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN C 292 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER C 208 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN C 287 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU C 317 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS C 289 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU C 319 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU C 291 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE C 359 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY C 262 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR C 382 " --> pdb=" O GLY C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.693A pdb=" N PHE D 169 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 116 through 122 Processing sheet with id=AB3, first strand: chain 'D' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE D 205 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR D 206 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN D 292 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER D 208 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN D 287 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU D 317 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS D 289 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU D 319 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU D 291 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE D 359 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY D 262 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 382 " --> pdb=" O GLY D 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE E 169 " --> pdb=" O SER E 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 116 through 122 Processing sheet with id=AB6, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE E 205 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR E 206 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN E 292 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER E 208 " --> pdb=" O ASN E 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN E 287 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU E 317 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS E 289 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU E 319 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU E 291 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE E 359 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY E 262 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR E 382 " --> pdb=" O GLY E 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE F 169 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 116 through 122 Processing sheet with id=AB9, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.261A pdb=" N ILE F 205 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR F 206 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN F 292 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER F 208 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN F 287 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU F 317 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS F 289 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU F 319 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU F 291 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE F 359 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY F 262 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 382 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE G 169 " --> pdb=" O SER G 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 116 through 122 Processing sheet with id=AC3, first strand: chain 'G' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE G 205 " --> pdb=" O PHE G 216 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR G 206 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN G 292 " --> pdb=" O TYR G 206 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER G 208 " --> pdb=" O ASN G 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN G 287 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU G 317 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS G 289 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU G 319 " --> pdb=" O CYS G 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU G 291 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE G 359 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY G 262 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR G 382 " --> pdb=" O GLY G 262 " (cutoff:3.500A) 755 hydrogen bonds defined for protein. 2160 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: 3.69 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 2338 1.28 - 1.35: 2290 1.35 - 1.42: 13 1.42 - 1.48: 2317 1.48 - 1.55: 4536 Bond restraints: 11494 Sorted by residual: bond pdb=" N LEU C 177 " pdb=" CA LEU C 177 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" N LEU D 177 " pdb=" CA LEU D 177 " ideal model delta sigma weight residual 1.456 1.502 -0.045 1.27e-02 6.20e+03 1.28e+01 bond pdb=" N LEU F 177 " pdb=" CA LEU F 177 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.27e-02 6.20e+03 1.27e+01 bond pdb=" N LEU G 177 " pdb=" CA LEU G 177 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.27e-02 6.20e+03 1.26e+01 bond pdb=" N LEU B 177 " pdb=" CA LEU B 177 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.27e-02 6.20e+03 1.26e+01 ... (remaining 11489 not shown) Histogram of bond angle deviations from ideal: 100.91 - 106.30: 140 106.30 - 111.69: 5445 111.69 - 117.08: 2541 117.08 - 122.47: 5870 122.47 - 127.87: 1943 Bond angle restraints: 15939 Sorted by residual: angle pdb=" N PRO F 403 " pdb=" CA PRO F 403 " pdb=" CB PRO F 403 " ideal model delta sigma weight residual 103.31 110.49 -7.18 8.90e-01 1.26e+00 6.50e+01 angle pdb=" N PRO G 403 " pdb=" CA PRO G 403 " pdb=" CB PRO G 403 " ideal model delta sigma weight residual 103.31 110.47 -7.16 8.90e-01 1.26e+00 6.48e+01 angle pdb=" N PRO B 403 " pdb=" CA PRO B 403 " pdb=" CB PRO B 403 " ideal model delta sigma weight residual 103.31 110.47 -7.16 8.90e-01 1.26e+00 6.47e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.31 110.46 -7.15 8.90e-01 1.26e+00 6.45e+01 angle pdb=" N PRO D 403 " pdb=" CA PRO D 403 " pdb=" CB PRO D 403 " ideal model delta sigma weight residual 103.31 110.45 -7.14 8.90e-01 1.26e+00 6.43e+01 ... (remaining 15934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.51: 5913 5.51 - 11.02: 639 11.02 - 16.52: 84 16.52 - 22.03: 14 22.03 - 27.54: 7 Dihedral angle restraints: 6657 sinusoidal: 0 harmonic: 6657 Sorted by residual: dihedral pdb=" CA GLN D 218 " pdb=" C GLN D 218 " pdb=" N PRO D 219 " pdb=" CA PRO D 219 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN B 218 " pdb=" C GLN B 218 " pdb=" N PRO B 219 " pdb=" CA PRO B 219 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN E 218 " pdb=" C GLN E 218 " pdb=" N PRO E 219 " pdb=" CA PRO E 219 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 6654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1358 0.038 - 0.076: 489 0.076 - 0.114: 234 0.114 - 0.153: 68 0.153 - 0.191: 28 Chirality restraints: 2177 Sorted by residual: chirality pdb=" CA PRO F 219 " pdb=" N PRO F 219 " pdb=" C PRO F 219 " pdb=" CB PRO F 219 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA PRO D 219 " pdb=" N PRO D 219 " pdb=" C PRO D 219 " pdb=" CB PRO D 219 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA PRO A 219 " pdb=" N PRO A 219 " pdb=" C PRO A 219 " pdb=" CB PRO A 219 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 2174 not shown) Planarity restraints: 2303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 134 " -0.027 2.00e-02 2.50e+03 5.08e-02 2.59e+01 pdb=" C LEU A 134 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU A 134 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL A 135 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 134 " 0.027 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C LEU G 134 " -0.088 2.00e-02 2.50e+03 pdb=" O LEU G 134 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL G 135 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 134 " 0.027 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C LEU E 134 " -0.088 2.00e-02 2.50e+03 pdb=" O LEU E 134 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL E 135 " 0.029 2.00e-02 2.50e+03 ... (remaining 2300 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 5755 2.96 - 3.45: 10927 3.45 - 3.93: 14513 3.93 - 4.42: 14813 4.42 - 4.90: 24141 Nonbonded interactions: 70149 Sorted by model distance: nonbonded pdb=" O SER B 115 " pdb=" N VAL B 135 " model vdw 2.477 2.520 nonbonded pdb=" O SER A 115 " pdb=" N VAL A 135 " model vdw 2.477 2.520 nonbonded pdb=" O SER F 115 " pdb=" N VAL F 135 " model vdw 2.477 2.520 nonbonded pdb=" O SER G 115 " pdb=" N VAL G 135 " model vdw 2.477 2.520 nonbonded pdb=" O SER E 115 " pdb=" N VAL E 135 " model vdw 2.477 2.520 ... (remaining 70144 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' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.340 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: 0.010 Extract box with map and model: 4.310 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 37.220 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 0.046 11494 Z= 0.359 Angle : 0.971 8.523 15939 Z= 0.625 Chirality : 0.053 0.191 2177 Planarity : 0.005 0.051 2303 Dihedral : 5.648 27.537 2303 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -3.63 (0.15), residues: 2268 helix: -1.55 (0.15), residues: 854 sheet: -3.04 (0.19), residues: 511 loop : -2.67 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.191 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0232 time to fit residues: 0.7204 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 30.0000 chunk 175 optimal weight: 40.0000 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 0.0670 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.0010 chunk 181 optimal weight: 20.0000 chunk 70 optimal weight: 40.0000 chunk 110 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 209 optimal weight: 30.0000 overall best weight: 5.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 11494 Z= 0.183 Angle : 0.517 5.702 15939 Z= 0.307 Chirality : 0.042 0.158 2177 Planarity : 0.002 0.007 2303 Dihedral : 4.566 23.958 2303 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.66 (0.18), residues: 2268 helix: 0.54 (0.18), residues: 924 sheet: -2.45 (0.19), residues: 581 loop : -1.83 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0206 time to fit residues: 0.7470 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.213 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 57 optimal weight: 0.1980 chunk 210 optimal weight: 30.0000 chunk 227 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 208 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 chunk 168 optimal weight: 40.0000 overall best weight: 9.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11494 Z= 0.287 Angle : 0.627 5.300 15939 Z= 0.388 Chirality : 0.043 0.166 2177 Planarity : 0.003 0.011 2303 Dihedral : 5.857 22.458 2303 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.87 (0.17), residues: 2268 helix: 0.09 (0.16), residues: 931 sheet: -2.06 (0.22), residues: 490 loop : -2.12 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0177 time to fit residues: 0.6352 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 109 optimal weight: 40.0000 chunk 23 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 210 optimal weight: 30.0000 chunk 223 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 overall best weight: 10.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.7414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 11494 Z= 0.279 Angle : 0.616 6.398 15939 Z= 0.378 Chirality : 0.042 0.157 2177 Planarity : 0.003 0.011 2303 Dihedral : 5.830 23.763 2303 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.26 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.59 (0.18), residues: 2268 helix: 0.92 (0.18), residues: 861 sheet: -2.19 (0.23), residues: 434 loop : -2.35 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0198 time to fit residues: 0.7151 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 chunk 166 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.8683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11494 Z= 0.370 Angle : 0.707 6.243 15939 Z= 0.445 Chirality : 0.044 0.152 2177 Planarity : 0.004 0.012 2303 Dihedral : 6.879 24.802 2303 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -2.70 (0.17), residues: 2268 helix: -0.03 (0.17), residues: 896 sheet: -2.48 (0.21), residues: 560 loop : -3.23 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0193 time to fit residues: 0.7132 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 20.0000 chunk 201 optimal weight: 50.0000 chunk 44 optimal weight: 30.0000 chunk 131 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 117 optimal weight: 20.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.9822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 11494 Z= 0.416 Angle : 0.786 7.834 15939 Z= 0.488 Chirality : 0.044 0.140 2177 Planarity : 0.005 0.024 2303 Dihedral : 7.465 32.569 2303 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 18.52 % Favored : 81.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.98 (0.15), residues: 2268 helix: -1.05 (0.16), residues: 875 sheet: -2.65 (0.21), residues: 455 loop : -4.24 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0202 time to fit residues: 0.7214 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 222 optimal weight: 7.9990 chunk 139 optimal weight: 50.0000 chunk 135 optimal weight: 50.0000 chunk 102 optimal weight: 40.0000 overall best weight: 10.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.9839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 11494 Z= 0.291 Angle : 0.617 6.300 15939 Z= 0.380 Chirality : 0.042 0.140 2177 Planarity : 0.003 0.011 2303 Dihedral : 6.339 23.470 2303 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.21 % Favored : 81.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -3.59 (0.16), residues: 2268 helix: -0.48 (0.17), residues: 854 sheet: -3.12 (0.19), residues: 525 loop : -3.79 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0195 time to fit residues: 0.6992 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 40.0000 chunk 88 optimal weight: 10.0000 chunk 132 optimal weight: 50.0000 chunk 67 optimal weight: 40.0000 chunk 43 optimal weight: 30.0000 chunk 141 optimal weight: 20.0000 chunk 151 optimal weight: 0.0670 chunk 110 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 202 optimal weight: 10.0000 overall best weight: 12.0134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 1.0199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 11494 Z= 0.318 Angle : 0.662 7.086 15939 Z= 0.406 Chirality : 0.043 0.138 2177 Planarity : 0.003 0.012 2303 Dihedral : 6.604 26.758 2303 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.60 % Favored : 78.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -3.89 (0.16), residues: 2268 helix: -0.66 (0.16), residues: 854 sheet: -3.35 (0.21), residues: 448 loop : -4.02 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0188 time to fit residues: 0.7282 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 63 optimal weight: 40.0000 chunk 187 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 206 optimal weight: 50.0000 chunk 136 optimal weight: 30.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 1.0196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 11494 Z= 0.253 Angle : 0.583 6.105 15939 Z= 0.356 Chirality : 0.042 0.144 2177 Planarity : 0.003 0.010 2303 Dihedral : 6.018 23.355 2303 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.59 % Favored : 82.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -3.55 (0.17), residues: 2268 helix: -0.19 (0.16), residues: 854 sheet: -3.53 (0.20), residues: 504 loop : -3.78 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0215 time to fit residues: 0.7333 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 20.0000 chunk 133 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 152 optimal weight: 20.0000 chunk 230 optimal weight: 30.0000 chunk 211 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 1.0194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 11494 Z= 0.204 Angle : 0.533 6.039 15939 Z= 0.319 Chirality : 0.042 0.143 2177 Planarity : 0.002 0.009 2303 Dihedral : 5.465 21.557 2303 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -3.08 (0.17), residues: 2268 helix: 0.29 (0.16), residues: 861 sheet: -3.20 (0.22), residues: 448 loop : -3.73 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.183 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0185 time to fit residues: 0.6598 Evaluate side-chains 12 residues out of total 293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.180 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 40.0000 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 188 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 50.0000 chunk 161 optimal weight: 20.0000 overall best weight: 7.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.042723 restraints weight = 13284.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.042112 restraints weight = 11293.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.042147 restraints weight = 11156.084| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 1.0247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 11494 Z= 0.203 Angle : 0.518 5.682 15939 Z= 0.313 Chirality : 0.042 0.143 2177 Planarity : 0.002 0.008 2303 Dihedral : 5.280 21.569 2303 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.36 % Favored : 83.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -2.90 (0.17), residues: 2268 helix: 0.49 (0.16), residues: 868 sheet: -3.16 (0.22), residues: 448 loop : -3.68 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.71 seconds wall clock time: 27 minutes 52.28 seconds (1672.28 seconds total)