Starting phenix.real_space_refine on Fri Mar 15 23:17:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/03_2024/6sh4_10193.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/03_2024/6sh4_10193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/03_2024/6sh4_10193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/03_2024/6sh4_10193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/03_2024/6sh4_10193.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh4_10193/03_2024/6sh4_10193.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 7693 2.51 5 N 2632 2.21 5 O 2632 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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12957 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Chain: "B" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Chain: "C" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Chain: "D" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Chain: "E" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Chain: "F" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Chain: "G" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1851 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1195 Unresolved non-hydrogen angles: 1528 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 8, 'TYR:plan': 16, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 617 Time building chain proxies: 7.79, per 1000 atoms: 0.60 Number of scatterers: 12957 At special positions: 0 Unit cell: (151.437, 148.26, 133.434, 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 2632 8.00 N 2632 7.00 C 7693 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: 5.24 Conformation dependent library (CDL) restraints added in 3.3 seconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4858 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 21 sheets defined 45.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.678A 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: 3.729A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 324 removed outlier: 3.849A 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 350 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.616A pdb=" N ALA A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 83 removed outlier: 4.503A pdb=" N GLY B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.678A 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: 3.729A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.848A 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 350 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.617A pdb=" N ALA B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.678A 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: 3.728A pdb=" N ASN C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.849A 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 350 Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 405 through 417 removed outlier: 4.015A pdb=" N CYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.617A pdb=" N ALA C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.121A pdb=" N ASP D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.678A 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: 3.729A pdb=" N ASN D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 324 removed outlier: 3.849A 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 350 Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.616A pdb=" N ALA D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.678A 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: 3.729A pdb=" N ASN E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 324 removed outlier: 3.849A 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 350 Processing helix chain 'E' and resid 390 through 402 Processing helix chain 'E' and resid 405 through 417 removed outlier: 4.015A pdb=" N CYS E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 411 " --> pdb=" O ASP E 407 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.617A pdb=" N ALA E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY F 56 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.509A pdb=" N LYS F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.678A 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: 3.729A pdb=" N ASN F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS F 305 " --> pdb=" O ASP F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 324 removed outlier: 3.849A 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 350 Processing helix chain 'F' and resid 390 through 402 Processing helix chain 'F' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS F 411 " --> pdb=" O ASP F 407 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.616A pdb=" N ALA F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS F 444 " --> pdb=" O HIS F 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 83 removed outlier: 4.502A pdb=" N GLY G 56 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 removed outlier: 3.510A pdb=" N LYS G 105 " --> pdb=" O THR G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 182 through 197 removed outlier: 4.120A pdb=" N ASP G 186 " --> pdb=" O HIS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.617A pdb=" N ILE G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.678A 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: 3.729A pdb=" N ASN G 304 " --> pdb=" O ASP G 300 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS G 305 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.850A 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 350 Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 405 through 417 removed outlier: 4.016A pdb=" N CYS G 409 " --> pdb=" O GLU G 405 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 410 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS G 411 " --> pdb=" O ASP G 407 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.616A pdb=" N ALA G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS G 444 " --> pdb=" O HIS G 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE A 169 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 152 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 122 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 208 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN A 292 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU A 319 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 291 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE A 359 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 261 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET A 362 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 263 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR A 364 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 265 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE A 380 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY A 262 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 382 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE B 169 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 152 " --> pdb=" O HIS B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 122 Processing sheet with id=AA6, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 208 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN B 292 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 317 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS B 289 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU B 319 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 291 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE B 359 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG B 261 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET B 362 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR B 263 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 364 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 265 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE B 380 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY B 262 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 382 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE C 169 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 152 " --> pdb=" O HIS C 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 122 Processing sheet with id=AA9, first strand: chain 'C' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER C 208 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASN C 292 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN C 287 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 317 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS C 289 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU C 319 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU C 291 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE C 359 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG C 261 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET C 362 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR C 263 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR C 364 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 265 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE C 380 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY C 262 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 382 " --> pdb=" O GLY C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE D 169 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 152 " --> pdb=" O HIS D 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 122 Processing sheet with id=AB3, first strand: chain 'D' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE D 205 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 208 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASN D 292 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN D 287 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU D 317 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS D 289 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU D 319 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 291 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE D 359 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG D 261 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET D 362 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR D 263 " --> pdb=" O MET D 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 364 " --> pdb=" O TYR D 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU D 265 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE D 380 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY D 262 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 382 " --> pdb=" O GLY D 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE E 169 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 152 " --> pdb=" O HIS E 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 115 through 122 Processing sheet with id=AB6, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE E 205 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER E 208 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN E 292 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN E 287 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU E 317 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS E 289 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU E 319 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU E 291 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE E 359 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG E 261 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET E 362 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR E 263 " --> pdb=" O MET E 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR E 364 " --> pdb=" O TYR E 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU E 265 " --> pdb=" O THR E 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE E 380 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY E 262 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR E 382 " --> pdb=" O GLY E 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 90 removed outlier: 4.589A pdb=" N PHE F 169 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 152 " --> pdb=" O HIS F 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 115 through 122 Processing sheet with id=AB9, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.072A pdb=" N ILE F 205 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER F 208 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASN F 292 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN F 287 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 317 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS F 289 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU F 319 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F 291 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE F 359 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG F 261 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET F 362 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR F 263 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR F 364 " --> pdb=" O TYR F 263 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU F 265 " --> pdb=" O THR F 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE F 380 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY F 262 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR F 382 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 84 through 90 removed outlier: 4.590A pdb=" N PHE G 169 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE G 152 " --> pdb=" O HIS G 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 122 Processing sheet with id=AC3, first strand: chain 'G' and resid 213 through 216 removed outlier: 4.073A pdb=" N ILE G 205 " --> pdb=" O PHE G 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER G 208 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN G 292 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN G 287 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU G 317 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS G 289 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU G 319 " --> pdb=" O CYS G 289 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU G 291 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE G 359 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG G 261 " --> pdb=" O THR G 360 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET G 362 " --> pdb=" O ARG G 261 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR G 263 " --> pdb=" O MET G 362 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR G 364 " --> pdb=" O TYR G 263 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU G 265 " --> pdb=" O THR G 364 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE G 380 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY G 262 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR G 382 " --> pdb=" O GLY G 262 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2667 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: 4.68 Time building geometry restraints manager: 5.68 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: 2632 1.28 - 1.35: 2590 1.35 - 1.42: 14 1.42 - 1.48: 2506 1.48 - 1.55: 5187 Bond restraints: 12929 Sorted by residual: bond pdb=" N VAL E 352 " pdb=" CA VAL E 352 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.38e+00 bond pdb=" N VAL G 352 " pdb=" CA VAL G 352 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.22e+00 bond pdb=" N VAL D 352 " pdb=" CA VAL D 352 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.22e+00 bond pdb=" N VAL C 352 " pdb=" CA VAL C 352 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.07e+00 bond pdb=" N VAL B 352 " pdb=" CA VAL B 352 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.99e+00 ... (remaining 12924 not shown) Histogram of bond angle deviations from ideal: 101.97 - 107.45: 272 107.45 - 112.94: 6829 112.94 - 118.42: 2905 118.42 - 123.90: 7635 123.90 - 129.38: 293 Bond angle restraints: 17934 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 103.31 110.43 -7.12 8.90e-01 1.26e+00 6.40e+01 angle pdb=" N PRO G 403 " pdb=" CA PRO G 403 " pdb=" CB PRO G 403 " ideal model delta sigma weight residual 103.31 110.38 -7.07 8.90e-01 1.26e+00 6.32e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.31 110.38 -7.07 8.90e-01 1.26e+00 6.31e+01 angle pdb=" N PRO D 403 " pdb=" CA PRO D 403 " pdb=" CB PRO D 403 " ideal model delta sigma weight residual 103.31 110.38 -7.07 8.90e-01 1.26e+00 6.31e+01 angle pdb=" N PRO B 403 " pdb=" CA PRO B 403 " pdb=" CB PRO B 403 " ideal model delta sigma weight residual 103.31 110.37 -7.06 8.90e-01 1.26e+00 6.30e+01 ... (remaining 17929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.87: 6317 3.87 - 7.74: 788 7.74 - 11.61: 280 11.61 - 15.47: 56 15.47 - 19.34: 21 Dihedral angle restraints: 7462 sinusoidal: 0 harmonic: 7462 Sorted by residual: dihedral pdb=" CA GLY B 378 " pdb=" C GLY B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLY C 378 " pdb=" C GLY C 378 " pdb=" N ARG C 379 " pdb=" CA ARG C 379 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLY A 378 " pdb=" C GLY A 378 " pdb=" N ARG A 379 " pdb=" CA ARG A 379 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 7459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1825 0.062 - 0.123: 442 0.123 - 0.185: 106 0.185 - 0.246: 28 0.246 - 0.308: 28 Chirality restraints: 2429 Sorted by residual: chirality pdb=" CA TYR E 80 " pdb=" N TYR E 80 " pdb=" C TYR E 80 " pdb=" CB TYR E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA TYR F 80 " pdb=" N TYR F 80 " pdb=" C TYR F 80 " pdb=" CB TYR F 80 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA TYR D 80 " pdb=" N TYR D 80 " pdb=" C TYR D 80 " pdb=" CB TYR D 80 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 2426 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 429 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C GLN E 429 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN E 429 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY E 430 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 429 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLN G 429 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN G 429 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY G 430 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 429 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLN D 429 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN D 429 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 430 " -0.014 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5550 2.90 - 3.40: 12337 3.40 - 3.90: 17529 3.90 - 4.40: 16867 4.40 - 4.90: 28472 Nonbonded interactions: 80755 Sorted by model distance: nonbonded pdb=" O LEU B 196 " pdb=" N THR B 198 " model vdw 2.405 2.520 nonbonded pdb=" O LEU G 196 " pdb=" N THR G 198 " model vdw 2.405 2.520 nonbonded pdb=" O LEU C 196 " pdb=" N THR C 198 " model vdw 2.405 2.520 nonbonded pdb=" O LEU F 196 " pdb=" N THR F 198 " model vdw 2.405 2.520 nonbonded pdb=" O LEU D 196 " pdb=" N THR D 198 " model vdw 2.405 2.520 ... (remaining 80750 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 No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.350 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: 0.030 Extract box with map and model: 4.360 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.260 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 0.040 12929 Z= 0.367 Angle : 1.005 11.924 17934 Z= 0.684 Chirality : 0.066 0.308 2429 Planarity : 0.004 0.024 2604 Dihedral : 5.132 19.343 2604 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.79 % Favored : 92.39 % 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: -2.94 (0.15), residues: 2576 helix: -0.50 (0.15), residues: 1064 sheet: -3.15 (0.18), residues: 574 loop : -2.69 (0.18), 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 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.442 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1078 time to fit residues: 21.9143 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 67 optimal weight: 0.0060 chunk 132 optimal weight: 40.0000 chunk 104 optimal weight: 0.1980 chunk 203 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 235 optimal weight: 0.0070 overall best weight: 3.0418 ------------------------------------------------------------------------------- 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: 0.7637 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 12929 Z= 0.136 Angle : 0.461 5.089 17934 Z= 0.279 Chirality : 0.042 0.128 2429 Planarity : 0.002 0.012 2604 Dihedral : 4.422 27.507 2604 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: -1.45 (0.17), residues: 2576 helix: 0.69 (0.16), residues: 1148 sheet: -2.62 (0.19), residues: 532 loop : -1.96 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.600 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1091 time to fit residues: 22.1425 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 235 optimal weight: 0.9980 chunk 254 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 80 optimal weight: 40.0000 chunk 189 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 12929 Z= 0.299 Angle : 0.661 6.425 17934 Z= 0.409 Chirality : 0.046 0.150 2429 Planarity : 0.004 0.013 2604 Dihedral : 5.996 30.202 2604 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.18 % Favored : 92.55 % 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 : 0.84 % 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: -1.67 (0.16), residues: 2576 helix: 0.39 (0.16), residues: 1120 sheet: -1.88 (0.19), residues: 623 loop : -2.42 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.447 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1073 time to fit residues: 21.7506 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 chunk 236 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 224 optimal weight: 8.9990 chunk 67 optimal weight: 0.0670 overall best weight: 5.2126 ------------------------------------------------------------------------------- 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: 0.7834 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 12929 Z= 0.175 Angle : 0.472 6.047 17934 Z= 0.285 Chirality : 0.042 0.140 2429 Planarity : 0.002 0.007 2604 Dihedral : 4.873 29.510 2604 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: -0.69 (0.17), residues: 2576 helix: 1.41 (0.17), residues: 1085 sheet: -1.31 (0.21), residues: 546 loop : -2.16 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1099 time to fit residues: 22.3127 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 213 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 127 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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: 0.7885 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 12929 Z= 0.262 Angle : 0.581 6.047 17934 Z= 0.357 Chirality : 0.045 0.151 2429 Planarity : 0.003 0.013 2604 Dihedral : 5.785 29.307 2604 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % 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: -1.04 (0.17), residues: 2576 helix: 0.81 (0.16), residues: 1099 sheet: -1.16 (0.22), residues: 581 loop : -2.22 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.444 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1104 time to fit residues: 22.2709 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 250 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 20 optimal weight: 40.0000 chunk 82 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 12929 Z= 0.165 Angle : 0.458 6.315 17934 Z= 0.276 Chirality : 0.042 0.137 2429 Planarity : 0.002 0.009 2604 Dihedral : 4.833 28.692 2604 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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: -0.41 (0.18), residues: 2576 helix: 1.57 (0.16), residues: 1099 sheet: -1.04 (0.22), residues: 588 loop : -2.08 (0.21), 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 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.489 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1118 time to fit residues: 22.8031 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 9.9990 chunk 28 optimal weight: 0.0060 chunk 142 optimal weight: 3.9990 chunk 182 optimal weight: 0.4980 chunk 141 optimal weight: 0.0770 chunk 210 optimal weight: 9.9990 chunk 139 optimal weight: 30.0000 chunk 249 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 overall best weight: 2.7158 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 12929 Z= 0.100 Angle : 0.391 5.625 17934 Z= 0.231 Chirality : 0.041 0.138 2429 Planarity : 0.001 0.008 2604 Dihedral : 4.074 27.516 2604 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % 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: 0.22 (0.18), residues: 2576 helix: 2.26 (0.17), residues: 1099 sheet: -0.74 (0.23), residues: 546 loop : -1.96 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.564 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1126 time to fit residues: 22.8413 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 48 optimal weight: 0.0670 chunk 158 optimal weight: 6.9990 chunk 170 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 overall best weight: 3.7124 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 12929 Z= 0.126 Angle : 0.410 5.900 17934 Z= 0.243 Chirality : 0.041 0.138 2429 Planarity : 0.002 0.008 2604 Dihedral : 4.123 26.761 2604 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % 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 : 0.00 % 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: 0.31 (0.18), residues: 2576 helix: 2.36 (0.17), residues: 1099 sheet: -0.74 (0.22), residues: 588 loop : -1.97 (0.21), 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 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1092 time to fit residues: 21.9223 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 8.9990 chunk 239 optimal weight: 0.0010 chunk 218 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 220 optimal weight: 0.1980 chunk 231 optimal weight: 5.9990 overall best weight: 2.4392 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 12929 Z= 0.093 Angle : 0.372 5.400 17934 Z= 0.218 Chirality : 0.041 0.135 2429 Planarity : 0.001 0.008 2604 Dihedral : 3.716 26.168 2604 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % 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: 0.60 (0.18), residues: 2576 helix: 2.65 (0.17), residues: 1099 sheet: -0.54 (0.22), residues: 588 loop : -1.92 (0.22), 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 52 TYR 0.000 0.000 TYR A 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.493 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1061 time to fit residues: 21.3283 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 150 optimal weight: 40.0000 chunk 116 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 237 optimal weight: 30.0000 chunk 205 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 12929 Z= 0.204 Angle : 0.486 6.319 17934 Z= 0.295 Chirality : 0.042 0.137 2429 Planarity : 0.002 0.009 2604 Dihedral : 4.706 27.339 2604 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % 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: 0.05 (0.18), residues: 2576 helix: 2.08 (0.16), residues: 1099 sheet: -0.83 (0.22), residues: 588 loop : -2.02 (0.22), 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 52 TYR 0.000 0.000 TYR A 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.320 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1050 time to fit residues: 21.0906 Evaluate side-chains 98 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 30 optimal weight: 0.0570 chunk 57 optimal weight: 0.0870 chunk 205 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 211 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 37 optimal weight: 50.0000 overall best weight: 5.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.055653 restraints weight = 78992.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056378 restraints weight = 56830.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.056826 restraints weight = 45201.284| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 12929 Z= 0.165 Angle : 0.439 5.864 17934 Z= 0.265 Chirality : 0.042 0.135 2429 Planarity : 0.002 0.010 2604 Dihedral : 4.468 28.331 2604 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.03 % Favored : 92.78 % 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: 0.09 (0.18), residues: 2576 helix: 2.23 (0.16), residues: 1092 sheet: -0.86 (0.22), residues: 588 loop : -2.10 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 52 TYR 0.000 0.000 TYR A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.06 seconds wall clock time: 30 minutes 49.58 seconds (1849.58 seconds total)