Starting phenix.real_space_refine on Sat Jun 28 11:09:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2n_18852/06_2025/8r2n_18852_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2n_18852/06_2025/8r2n_18852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r2n_18852/06_2025/8r2n_18852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2n_18852/06_2025/8r2n_18852.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2n_18852/06_2025/8r2n_18852_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2n_18852/06_2025/8r2n_18852_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 P 36 5.49 5 S 60 5.16 5 C 20556 2.51 5 N 5820 2.21 5 O 6753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33237 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "B" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "C" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "D" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "E" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "F" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "G" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "H" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "I" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "J" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "K" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "L" Number of atoms: 2692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 353, 2669 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 336} bond proxies already assigned to first conformer: 2687 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Time building chain proxies: 33.91, per 1000 atoms: 1.02 Number of scatterers: 33237 At special positions: 0 Unit cell: (104.25, 104.25, 270.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 S 60 16.00 P 36 15.00 O 6753 8.00 N 5820 7.00 C 20556 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 - 3.00 Amino acid : True - 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.50 Conformation dependent library (CDL) restraints added in 8.2 seconds 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 60 sheets defined 42.7% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.063A pdb=" N ARG A 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.721A pdb=" N ASN A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 Processing helix chain 'A' and resid 148 through 158 removed outlier: 3.625A pdb=" N VAL A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.502A pdb=" N LEU A 185 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 244 removed outlier: 3.554A pdb=" N THR A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.607A pdb=" N GLU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 312 removed outlier: 3.527A pdb=" N ALA A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 316 through 323 removed outlier: 3.707A pdb=" N GLN A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 363 through 375 Processing helix chain 'B' and resid 82 through 86 removed outlier: 4.055A pdb=" N ARG B 86 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 3.574A pdb=" N ASN B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.757A pdb=" N VAL B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.590A pdb=" N LEU B 185 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 244 removed outlier: 3.588A pdb=" N THR B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.643A pdb=" N GLU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 312 removed outlier: 4.191A pdb=" N LEU B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 316 through 323 removed outlier: 3.694A pdb=" N GLN B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 363 through 375 Processing helix chain 'C' and resid 82 through 86 removed outlier: 4.083A pdb=" N ARG C 86 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.629A pdb=" N ASN C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 Processing helix chain 'C' and resid 148 through 158 removed outlier: 3.736A pdb=" N VAL C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 180 Processing helix chain 'C' and resid 181 through 185 removed outlier: 3.518A pdb=" N LEU C 185 " --> pdb=" O ASP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 244 removed outlier: 3.571A pdb=" N THR C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.640A pdb=" N GLU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 312 removed outlier: 3.517A pdb=" N ALA C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.723A pdb=" N GLN C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 335 through 347 Processing helix chain 'C' and resid 363 through 375 Processing helix chain 'D' and resid 82 through 86 removed outlier: 4.111A pdb=" N ARG D 86 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 97 removed outlier: 3.709A pdb=" N ASN D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 Processing helix chain 'D' and resid 148 through 158 removed outlier: 3.704A pdb=" N VAL D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 228 through 244 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.606A pdb=" N GLU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 312 removed outlier: 3.610A pdb=" N ALA D 296 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 316 through 323 removed outlier: 3.665A pdb=" N GLN D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 333 Processing helix chain 'D' and resid 335 through 347 Processing helix chain 'D' and resid 363 through 375 Processing helix chain 'E' and resid 82 through 86 removed outlier: 4.083A pdb=" N ARG E 86 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 removed outlier: 3.748A pdb=" N ASN E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 148 through 158 removed outlier: 3.652A pdb=" N VAL E 155 " --> pdb=" O ALA E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 180 Processing helix chain 'E' and resid 228 through 244 removed outlier: 3.554A pdb=" N THR E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.648A pdb=" N GLU E 256 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 312 removed outlier: 3.540A pdb=" N ALA E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 298 " --> pdb=" O CYS E 294 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 316 through 321 Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 335 through 347 Processing helix chain 'E' and resid 363 through 375 Processing helix chain 'F' and resid 82 through 86 removed outlier: 4.112A pdb=" N ARG F 86 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 97 removed outlier: 3.664A pdb=" N ASN F 97 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 Processing helix chain 'F' and resid 148 through 158 removed outlier: 3.689A pdb=" N VAL F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 180 Processing helix chain 'F' and resid 181 through 185 Processing helix chain 'F' and resid 228 through 244 removed outlier: 3.693A pdb=" N THR F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.566A pdb=" N GLU F 256 " --> pdb=" O HIS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 312 removed outlier: 3.512A pdb=" N ALA F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU F 297 " --> pdb=" O ALA F 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE F 298 " --> pdb=" O CYS F 294 " (cutoff:3.500A) Proline residue: F 303 - end of helix Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.682A pdb=" N GLN F 322 " --> pdb=" O VAL F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 Processing helix chain 'F' and resid 335 through 347 Processing helix chain 'F' and resid 363 through 375 Processing helix chain 'G' and resid 82 through 86 removed outlier: 4.132A pdb=" N ARG G 86 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 114 through 130 Processing helix chain 'G' and resid 148 through 158 removed outlier: 3.751A pdb=" N VAL G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 180 Processing helix chain 'G' and resid 181 through 185 removed outlier: 3.553A pdb=" N LEU G 185 " --> pdb=" O ASP G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 244 removed outlier: 3.597A pdb=" N THR G 243 " --> pdb=" O GLU G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 262 removed outlier: 3.725A pdb=" N GLU G 256 " --> pdb=" O HIS G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 312 removed outlier: 4.209A pdb=" N LEU G 297 " --> pdb=" O ALA G 293 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE G 298 " --> pdb=" O CYS G 294 " (cutoff:3.500A) Proline residue: G 303 - end of helix Processing helix chain 'G' and resid 316 through 323 removed outlier: 3.723A pdb=" N GLN G 322 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 333 Processing helix chain 'G' and resid 335 through 347 Processing helix chain 'G' and resid 363 through 375 Processing helix chain 'H' and resid 82 through 86 removed outlier: 4.041A pdb=" N ARG H 86 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 97 removed outlier: 3.622A pdb=" N ASN H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 130 Processing helix chain 'H' and resid 148 through 158 removed outlier: 3.688A pdb=" N VAL H 155 " --> pdb=" O ALA H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 180 Processing helix chain 'H' and resid 181 through 185 removed outlier: 3.520A pdb=" N LEU H 185 " --> pdb=" O ASP H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 244 removed outlier: 3.625A pdb=" N THR H 243 " --> pdb=" O GLU H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 262 removed outlier: 3.536A pdb=" N GLU H 256 " --> pdb=" O HIS H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 312 removed outlier: 3.529A pdb=" N ALA H 296 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU H 297 " --> pdb=" O ALA H 293 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE H 298 " --> pdb=" O CYS H 294 " (cutoff:3.500A) Proline residue: H 303 - end of helix Processing helix chain 'H' and resid 316 through 323 removed outlier: 3.727A pdb=" N GLN H 322 " --> pdb=" O VAL H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 333 Processing helix chain 'H' and resid 335 through 347 Processing helix chain 'H' and resid 363 through 375 Processing helix chain 'I' and resid 82 through 86 removed outlier: 4.080A pdb=" N ARG I 86 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 97 removed outlier: 3.650A pdb=" N ASN I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 130 Processing helix chain 'I' and resid 148 through 158 removed outlier: 3.696A pdb=" N VAL I 155 " --> pdb=" O ALA I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 180 Processing helix chain 'I' and resid 181 through 185 removed outlier: 3.573A pdb=" N LEU I 185 " --> pdb=" O ASP I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 244 removed outlier: 3.551A pdb=" N THR I 243 " --> pdb=" O GLU I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 262 removed outlier: 3.730A pdb=" N GLU I 256 " --> pdb=" O HIS I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 312 removed outlier: 3.599A pdb=" N ALA I 296 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU I 297 " --> pdb=" O ALA I 293 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE I 298 " --> pdb=" O CYS I 294 " (cutoff:3.500A) Proline residue: I 303 - end of helix Processing helix chain 'I' and resid 316 through 323 removed outlier: 3.732A pdb=" N GLN I 322 " --> pdb=" O VAL I 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 333 Processing helix chain 'I' and resid 335 through 347 Processing helix chain 'I' and resid 363 through 375 Processing helix chain 'J' and resid 82 through 86 removed outlier: 4.114A pdb=" N ARG J 86 " --> pdb=" O ALA J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 97 removed outlier: 3.662A pdb=" N ASN J 97 " --> pdb=" O ASP J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 130 Processing helix chain 'J' and resid 148 through 158 removed outlier: 3.711A pdb=" N VAL J 155 " --> pdb=" O ALA J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 180 Processing helix chain 'J' and resid 181 through 185 Processing helix chain 'J' and resid 228 through 244 removed outlier: 3.584A pdb=" N THR J 243 " --> pdb=" O GLU J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 262 removed outlier: 3.603A pdb=" N GLU J 256 " --> pdb=" O HIS J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 312 removed outlier: 3.561A pdb=" N ALA J 296 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU J 297 " --> pdb=" O ALA J 293 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE J 298 " --> pdb=" O CYS J 294 " (cutoff:3.500A) Proline residue: J 303 - end of helix Processing helix chain 'J' and resid 316 through 323 removed outlier: 3.718A pdb=" N GLN J 322 " --> pdb=" O VAL J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 333 Processing helix chain 'J' and resid 335 through 347 Processing helix chain 'J' and resid 363 through 375 Processing helix chain 'K' and resid 82 through 86 removed outlier: 4.105A pdb=" N ARG K 86 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 97 removed outlier: 3.723A pdb=" N ASN K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 130 Processing helix chain 'K' and resid 148 through 158 removed outlier: 3.745A pdb=" N VAL K 155 " --> pdb=" O ALA K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 180 Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.541A pdb=" N LEU K 185 " --> pdb=" O ASP K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 242 Processing helix chain 'K' and resid 250 through 262 removed outlier: 3.710A pdb=" N GLU K 256 " --> pdb=" O HIS K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 312 removed outlier: 4.307A pdb=" N LEU K 297 " --> pdb=" O ALA K 293 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE K 298 " --> pdb=" O CYS K 294 " (cutoff:3.500A) Proline residue: K 303 - end of helix Processing helix chain 'K' and resid 316 through 323 removed outlier: 3.706A pdb=" N GLN K 322 " --> pdb=" O VAL K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 333 Processing helix chain 'K' and resid 335 through 347 Processing helix chain 'K' and resid 363 through 375 Processing helix chain 'L' and resid 82 through 86 removed outlier: 4.122A pdb=" N ARG L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 97 removed outlier: 3.605A pdb=" N ASN L 97 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 130 Processing helix chain 'L' and resid 148 through 158 removed outlier: 3.756A pdb=" N VAL L 155 " --> pdb=" O ALA L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 180 Processing helix chain 'L' and resid 181 through 185 Processing helix chain 'L' and resid 228 through 244 removed outlier: 3.649A pdb=" N THR L 243 " --> pdb=" O GLU L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 262 removed outlier: 3.733A pdb=" N GLU L 256 " --> pdb=" O HIS L 252 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS L 258 " --> pdb=" O VAL L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 312 removed outlier: 3.504A pdb=" N ALA L 296 " --> pdb=" O ARG L 292 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU L 297 " --> pdb=" O ALA L 293 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE L 298 " --> pdb=" O CYS L 294 " (cutoff:3.500A) Proline residue: L 303 - end of helix Processing helix chain 'L' and resid 316 through 323 removed outlier: 3.727A pdb=" N GLN L 322 " --> pdb=" O VAL L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 333 Processing helix chain 'L' and resid 335 through 347 Processing helix chain 'L' and resid 363 through 375 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 225 removed outlier: 5.994A pdb=" N LEU A 198 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR A 327 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE A 200 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 277 Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 67 Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 225 removed outlier: 6.360A pdb=" N ILE B 324 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 272 through 277 Processing sheet with id=AB2, first strand: chain 'C' and resid 62 through 67 Processing sheet with id=AB3, first strand: chain 'C' and resid 88 through 90 Processing sheet with id=AB4, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AB5, first strand: chain 'C' and resid 222 through 225 removed outlier: 3.502A pdb=" N ILE C 225 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU C 198 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR C 327 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE C 200 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 324 " --> pdb=" O ARG C 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 272 through 277 Processing sheet with id=AB7, first strand: chain 'D' and resid 62 through 67 removed outlier: 6.368A pdb=" N VAL D 37 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL D 140 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL D 39 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLY D 142 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE D 41 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AB9, first strand: chain 'D' and resid 107 through 108 Processing sheet with id=AC1, first strand: chain 'D' and resid 222 through 225 removed outlier: 6.299A pdb=" N ILE D 324 " --> pdb=" O ARG D 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 272 through 277 removed outlier: 3.501A pdb=" N LYS D 280 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 62 through 67 Processing sheet with id=AC4, first strand: chain 'E' and resid 88 through 90 Processing sheet with id=AC5, first strand: chain 'E' and resid 107 through 108 Processing sheet with id=AC6, first strand: chain 'E' and resid 222 through 225 removed outlier: 6.329A pdb=" N ILE E 324 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 272 through 277 removed outlier: 3.508A pdb=" N LYS E 280 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 62 through 67 Processing sheet with id=AC9, first strand: chain 'F' and resid 88 through 90 Processing sheet with id=AD1, first strand: chain 'F' and resid 107 through 108 Processing sheet with id=AD2, first strand: chain 'F' and resid 222 through 225 removed outlier: 6.332A pdb=" N ILE F 324 " --> pdb=" O ARG F 355 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 272 through 277 removed outlier: 3.511A pdb=" N LYS F 280 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 62 through 67 Processing sheet with id=AD5, first strand: chain 'G' and resid 88 through 90 Processing sheet with id=AD6, first strand: chain 'G' and resid 107 through 108 Processing sheet with id=AD7, first strand: chain 'G' and resid 222 through 225 removed outlier: 3.554A pdb=" N ILE G 225 " --> pdb=" O SER G 207 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU G 198 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR G 327 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE G 200 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE G 324 " --> pdb=" O ARG G 355 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 272 through 277 Processing sheet with id=AD9, first strand: chain 'H' and resid 62 through 67 Processing sheet with id=AE1, first strand: chain 'H' and resid 88 through 90 Processing sheet with id=AE2, first strand: chain 'H' and resid 107 through 108 Processing sheet with id=AE3, first strand: chain 'H' and resid 222 through 225 removed outlier: 6.009A pdb=" N LEU H 198 " --> pdb=" O ILE H 325 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR H 327 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE H 200 " --> pdb=" O THR H 327 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE H 324 " --> pdb=" O ARG H 355 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 272 through 277 removed outlier: 3.516A pdb=" N LYS H 280 " --> pdb=" O ILE H 277 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 62 through 67 Processing sheet with id=AE6, first strand: chain 'I' and resid 88 through 90 Processing sheet with id=AE7, first strand: chain 'I' and resid 107 through 108 Processing sheet with id=AE8, first strand: chain 'I' and resid 222 through 225 removed outlier: 3.527A pdb=" N ILE I 225 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE I 324 " --> pdb=" O ARG I 355 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 272 through 277 Processing sheet with id=AF1, first strand: chain 'J' and resid 62 through 67 Processing sheet with id=AF2, first strand: chain 'J' and resid 88 through 90 Processing sheet with id=AF3, first strand: chain 'J' and resid 107 through 108 Processing sheet with id=AF4, first strand: chain 'J' and resid 222 through 225 removed outlier: 6.336A pdb=" N ILE J 324 " --> pdb=" O ARG J 355 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 272 through 277 Processing sheet with id=AF6, first strand: chain 'K' and resid 62 through 67 Processing sheet with id=AF7, first strand: chain 'K' and resid 88 through 90 Processing sheet with id=AF8, first strand: chain 'K' and resid 107 through 108 Processing sheet with id=AF9, first strand: chain 'K' and resid 222 through 225 removed outlier: 3.504A pdb=" N ILE K 225 " --> pdb=" O SER K 207 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU K 198 " --> pdb=" O ILE K 325 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR K 327 " --> pdb=" O LEU K 198 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE K 200 " --> pdb=" O THR K 327 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE K 324 " --> pdb=" O ARG K 355 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 272 through 277 Processing sheet with id=AG2, first strand: chain 'L' and resid 62 through 67 Processing sheet with id=AG3, first strand: chain 'L' and resid 88 through 90 Processing sheet with id=AG4, first strand: chain 'L' and resid 107 through 108 Processing sheet with id=AG5, first strand: chain 'L' and resid 222 through 225 removed outlier: 6.064A pdb=" N LEU L 198 " --> pdb=" O ILE L 325 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR L 327 " --> pdb=" O LEU L 198 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE L 200 " --> pdb=" O THR L 327 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE L 324 " --> pdb=" O ARG L 355 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 272 through 277 removed outlier: 3.537A pdb=" N LYS L 280 " --> pdb=" O ILE L 277 " (cutoff:3.500A) 1693 hydrogen bonds defined for protein. 4611 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: 13.24 Time building geometry restraints manager: 9.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11064 1.34 - 1.46: 5847 1.46 - 1.58: 16245 1.58 - 1.69: 60 1.69 - 1.81: 72 Bond restraints: 33288 Sorted by residual: bond pdb=" C4 ATP B 400 " pdb=" C5 ATP B 400 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.49e+01 bond pdb=" C4 ATP I 400 " pdb=" C5 ATP I 400 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP K 400 " pdb=" C5 ATP K 400 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.45e+01 bond pdb=" C4 ATP D 400 " pdb=" C5 ATP D 400 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" C4 ATP H 400 " pdb=" C5 ATP H 400 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.43e+01 ... (remaining 33283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 45011 3.50 - 7.01: 252 7.01 - 10.51: 37 10.51 - 14.02: 12 14.02 - 17.52: 12 Bond angle restraints: 45324 Sorted by residual: angle pdb=" PB ATP F 400 " pdb=" O3B ATP F 400 " pdb=" PG ATP F 400 " ideal model delta sigma weight residual 139.87 122.35 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" PB ATP D 400 " pdb=" O3B ATP D 400 " pdb=" PG ATP D 400 " ideal model delta sigma weight residual 139.87 122.61 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PB ATP E 400 " pdb=" O3B ATP E 400 " pdb=" PG ATP E 400 " ideal model delta sigma weight residual 139.87 123.20 16.67 1.00e+00 1.00e+00 2.78e+02 angle pdb=" PB ATP I 400 " pdb=" O3B ATP I 400 " pdb=" PG ATP I 400 " ideal model delta sigma weight residual 139.87 123.31 16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PB ATP B 400 " pdb=" O3B ATP B 400 " pdb=" PG ATP B 400 " ideal model delta sigma weight residual 139.87 123.34 16.53 1.00e+00 1.00e+00 2.73e+02 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17703 17.99 - 35.99: 1984 35.99 - 53.98: 491 53.98 - 71.98: 112 71.98 - 89.97: 62 Dihedral angle restraints: 20352 sinusoidal: 8196 harmonic: 12156 Sorted by residual: dihedral pdb=" CA ASP E 92 " pdb=" CB ASP E 92 " pdb=" CG ASP E 92 " pdb=" OD1 ASP E 92 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG G 138 " pdb=" CD ARG G 138 " pdb=" NE ARG G 138 " pdb=" CZ ARG G 138 " ideal model delta sinusoidal sigma weight residual -180.00 -135.23 -44.77 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG G 374 " pdb=" CD ARG G 374 " pdb=" NE ARG G 374 " pdb=" CZ ARG G 374 " ideal model delta sinusoidal sigma weight residual 180.00 135.67 44.33 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 20349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2658 0.028 - 0.057: 1617 0.057 - 0.085: 500 0.085 - 0.114: 367 0.114 - 0.142: 102 Chirality restraints: 5244 Sorted by residual: chirality pdb=" CB ILE C 191 " pdb=" CA ILE C 191 " pdb=" CG1 ILE C 191 " pdb=" CG2 ILE C 191 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CB ILE F 191 " pdb=" CA ILE F 191 " pdb=" CG1 ILE F 191 " pdb=" CG2 ILE F 191 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CB ILE I 191 " pdb=" CA ILE I 191 " pdb=" CG1 ILE I 191 " pdb=" CG2 ILE I 191 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 5241 not shown) Planarity restraints: 5904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 169 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO G 170 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 170 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 170 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 169 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO D 170 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 170 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 170 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 169 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO E 170 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 170 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 170 " -0.021 5.00e-02 4.00e+02 ... (remaining 5901 not shown) Histogram of nonbonded interaction distances: 0.17 - 1.12: 18 1.12 - 2.06: 110 2.06 - 3.01: 17843 3.01 - 3.95: 91203 3.95 - 4.90: 184982 Warning: very small nonbonded interaction distances. Nonbonded interactions: 294156 Sorted by model distance: nonbonded pdb=" O HOH K 510 " pdb=" O HOH K 511 " model vdw 0.173 3.040 nonbonded pdb=" O HOH G 511 " pdb=" O HOH G 512 " model vdw 0.173 3.040 nonbonded pdb=" O HOH C 511 " pdb=" O HOH C 513 " model vdw 0.174 3.040 nonbonded pdb=" O HOH H 510 " pdb=" O HOH H 511 " model vdw 0.175 3.040 nonbonded pdb=" O HOH F 511 " pdb=" O HOH F 512 " model vdw 0.175 3.040 ... (remaining 294151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'B' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'C' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'D' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'E' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'F' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'G' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'H' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'I' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'J' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'K' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) selection = (chain 'L' and (resid 34 through 45 or resid 47 through 122 or resid 124 through \ 252 or resid 254 through 361 or resid 363 through 386 or resid 400 through 401) \ ) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 1.430 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 97.720 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.210 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 0.081 33312 Z= 0.335 Angle : 0.779 17.525 45324 Z= 0.551 Chirality : 0.045 0.142 5244 Planarity : 0.004 0.040 5904 Dihedral : 16.656 89.974 12624 Min Nonbonded Distance : 0.173 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.25 % Allowed : 8.98 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.92 (0.11), residues: 4260 helix: -2.44 (0.10), residues: 1692 sheet: -2.03 (0.16), residues: 708 loop : -1.13 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 381 HIS 0.004 0.001 HIS B 114 PHE 0.013 0.001 PHE E 121 TYR 0.007 0.001 TYR H 263 ARG 0.009 0.001 ARG G 119 Details of bonding type rmsd hydrogen bonds : bond 0.15716 ( 1693) hydrogen bonds : angle 7.61175 ( 4611) covalent geometry : bond 0.00504 (33288) covalent geometry : angle 0.77902 (45324) Misc. bond : bond 0.00115 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 421 time to evaluate : 3.909 Fit side-chains REVERT: A 184 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8168 (ttp80) REVERT: A 385 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8446 (pp) REVERT: B 38 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8911 (mt) REVERT: B 164 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: B 385 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8109 (pp) REVERT: C 62 ILE cc_start: 0.8822 (mm) cc_final: 0.8611 (mm) REVERT: C 180 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8019 (ttt180) REVERT: C 385 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8126 (pp) REVERT: D 164 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: D 385 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8328 (pp) REVERT: F 180 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7732 (ttt180) REVERT: G 385 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8508 (pp) REVERT: I 62 ILE cc_start: 0.8825 (mm) cc_final: 0.8601 (mm) REVERT: I 180 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8043 (ttt180) REVERT: K 355 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7609 (ttp-110) REVERT: K 385 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8545 (pp) REVERT: L 93 ASP cc_start: 0.7766 (t0) cc_final: 0.7459 (t0) outliers start: 99 outliers final: 60 residues processed: 502 average time/residue: 0.4543 time to fit residues: 370.1717 Evaluate side-chains 457 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 385 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 327 THR Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 GLN Chi-restraints excluded: chain J residue 327 THR Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 0.7980 chunk 318 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 329 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 381 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 323 ASN C 100 HIS C 123 GLN A D 85 ASN D 100 HIS F 100 HIS F 234 GLN G 85 ASN H 123 GLN A H 150 GLN I 109 HIS J 109 HIS K 246 ASN L 85 ASN L 100 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113253 restraints weight = 144638.587| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.18 r_work: 0.2562 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33312 Z= 0.143 Angle : 0.526 6.851 45324 Z= 0.264 Chirality : 0.045 0.146 5244 Planarity : 0.005 0.060 5904 Dihedral : 9.450 89.675 5244 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.04 % Allowed : 11.08 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.12), residues: 4260 helix: -1.04 (0.12), residues: 1692 sheet: -1.48 (0.15), residues: 792 loop : -0.72 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 381 HIS 0.002 0.001 HIS A 124 PHE 0.014 0.001 PHE I 121 TYR 0.016 0.001 TYR C 361 ARG 0.007 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 1693) hydrogen bonds : angle 5.78365 ( 4611) covalent geometry : bond 0.00337 (33288) covalent geometry : angle 0.52627 (45324) Misc. bond : bond 0.00190 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 450 time to evaluate : 3.489 Fit side-chains REVERT: A 237 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: A 385 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8377 (pp) REVERT: B 385 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.7792 (pp) REVERT: C 62 ILE cc_start: 0.8672 (mm) cc_final: 0.8471 (mm) REVERT: C 164 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: C 385 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7856 (pp) REVERT: D 97 ASN cc_start: 0.8594 (m110) cc_final: 0.8341 (m110) REVERT: D 107 MET cc_start: 0.8572 (mtp) cc_final: 0.8341 (ttt) REVERT: D 385 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8147 (pp) REVERT: E 355 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7847 (ptt180) REVERT: G 164 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: G 350 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: G 355 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7894 (ttp-110) REVERT: G 361 TYR cc_start: 0.9188 (p90) cc_final: 0.8961 (p90) REVERT: G 385 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8133 (pp) REVERT: I 62 ILE cc_start: 0.8719 (mm) cc_final: 0.8490 (mm) REVERT: I 89 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8635 (mt) REVERT: I 180 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7338 (ttm170) REVERT: J 246 ASN cc_start: 0.8336 (t0) cc_final: 0.7971 (t0) REVERT: K 385 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8164 (pp) REVERT: L 93 ASP cc_start: 0.8404 (t0) cc_final: 0.7972 (t0) outliers start: 92 outliers final: 60 residues processed: 516 average time/residue: 0.4727 time to fit residues: 394.4135 Evaluate side-chains 483 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 411 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 GLN Chi-restraints excluded: chain J residue 350 GLU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 263 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN D 85 ASN G 85 ASN I 109 HIS J 322 GLN K 246 ASN K 323 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113946 restraints weight = 136289.169| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.04 r_work: 0.2611 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33312 Z= 0.156 Angle : 0.513 6.688 45324 Z= 0.255 Chirality : 0.045 0.134 5244 Planarity : 0.004 0.052 5904 Dihedral : 8.951 83.145 5204 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.10 % Allowed : 12.19 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.22 (0.12), residues: 4260 helix: -0.57 (0.12), residues: 1692 sheet: -1.43 (0.15), residues: 816 loop : -0.47 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.002 0.000 HIS I 109 PHE 0.012 0.001 PHE I 121 TYR 0.014 0.001 TYR G 361 ARG 0.007 0.000 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 1693) hydrogen bonds : angle 5.57588 ( 4611) covalent geometry : bond 0.00377 (33288) covalent geometry : angle 0.51313 (45324) Misc. bond : bond 0.00183 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 436 time to evaluate : 3.830 Fit side-chains REVERT: A 107 MET cc_start: 0.9196 (mmm) cc_final: 0.8974 (mmm) REVERT: A 355 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7840 (ptt180) REVERT: B 385 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7852 (pp) REVERT: C 62 ILE cc_start: 0.8681 (mm) cc_final: 0.8478 (mm) REVERT: C 164 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: C 184 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7854 (mtm110) REVERT: C 355 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7617 (ptt180) REVERT: C 385 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7854 (pp) REVERT: D 97 ASN cc_start: 0.8607 (m110) cc_final: 0.8338 (m110) REVERT: D 184 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8209 (ttp80) REVERT: D 385 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8197 (pp) REVERT: G 164 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: G 350 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: G 379 ASN cc_start: 0.9186 (p0) cc_final: 0.8932 (p0) REVERT: G 385 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8198 (pp) REVERT: I 62 ILE cc_start: 0.8732 (mm) cc_final: 0.8505 (mm) REVERT: I 89 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8650 (mt) REVERT: J 246 ASN cc_start: 0.8359 (t0) cc_final: 0.7984 (t0) REVERT: J 378 GLU cc_start: 0.8803 (tp30) cc_final: 0.8558 (tp30) REVERT: K 385 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8273 (pp) REVERT: L 93 ASP cc_start: 0.8323 (t0) cc_final: 0.7887 (t0) outliers start: 94 outliers final: 59 residues processed: 501 average time/residue: 0.4983 time to fit residues: 401.5843 Evaluate side-chains 469 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 401 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 GLN Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 402 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 338 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 chunk 188 optimal weight: 0.5980 chunk 208 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN B 85 ASN D 85 ASN I 109 HIS K 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114865 restraints weight = 159380.961| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.40 r_work: 0.2613 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33312 Z= 0.131 Angle : 0.491 6.202 45324 Z= 0.243 Chirality : 0.045 0.133 5244 Planarity : 0.004 0.062 5904 Dihedral : 8.363 86.700 5183 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.07 % Allowed : 12.92 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.75 (0.12), residues: 4260 helix: -0.20 (0.12), residues: 1692 sheet: -1.11 (0.15), residues: 792 loop : -0.25 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 381 HIS 0.002 0.000 HIS A 124 PHE 0.010 0.001 PHE I 121 TYR 0.010 0.001 TYR D 361 ARG 0.007 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.02640 ( 1693) hydrogen bonds : angle 5.37527 ( 4611) covalent geometry : bond 0.00313 (33288) covalent geometry : angle 0.49052 (45324) Misc. bond : bond 0.00148 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 439 time to evaluate : 5.531 Fit side-chains REVERT: A 107 MET cc_start: 0.9177 (mmm) cc_final: 0.8972 (mmm) REVERT: A 355 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7818 (ptt180) REVERT: B 385 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.7787 (pp) REVERT: C 164 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: C 184 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7843 (mtp180) REVERT: C 385 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7780 (pp) REVERT: D 97 ASN cc_start: 0.8604 (m110) cc_final: 0.8341 (m110) REVERT: D 274 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8614 (tmtt) REVERT: D 385 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8192 (pp) REVERT: F 355 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7822 (ptt180) REVERT: G 350 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: G 379 ASN cc_start: 0.9178 (p0) cc_final: 0.8942 (p0) REVERT: G 385 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8180 (pp) REVERT: J 246 ASN cc_start: 0.8335 (t0) cc_final: 0.7952 (t0) REVERT: K 385 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8191 (pp) REVERT: L 93 ASP cc_start: 0.8314 (t0) cc_final: 0.7939 (t0) outliers start: 93 outliers final: 63 residues processed: 501 average time/residue: 0.5805 time to fit residues: 469.0546 Evaluate side-chains 479 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 408 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 GLN Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 258 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 378 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 361 optimal weight: 0.0060 chunk 353 optimal weight: 0.0050 overall best weight: 0.7814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN I 97 ASN K 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116929 restraints weight = 135469.564| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.92 r_work: 0.2961 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33312 Z= 0.125 Angle : 0.484 7.888 45324 Z= 0.240 Chirality : 0.045 0.133 5244 Planarity : 0.004 0.062 5904 Dihedral : 8.226 89.080 5179 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.84 % Allowed : 14.01 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.46 (0.12), residues: 4260 helix: 0.06 (0.12), residues: 1704 sheet: -0.99 (0.15), residues: 792 loop : -0.10 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 381 HIS 0.002 0.000 HIS A 124 PHE 0.009 0.001 PHE I 121 TYR 0.023 0.001 TYR C 361 ARG 0.004 0.000 ARG F 242 Details of bonding type rmsd hydrogen bonds : bond 0.02582 ( 1693) hydrogen bonds : angle 5.26895 ( 4611) covalent geometry : bond 0.00296 (33288) covalent geometry : angle 0.48444 (45324) Misc. bond : bond 0.00145 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 437 time to evaluate : 3.904 Fit side-chains REVERT: B 385 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.7952 (pp) REVERT: C 184 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8085 (mtp180) REVERT: C 385 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.7980 (pp) REVERT: D 97 ASN cc_start: 0.8687 (m110) cc_final: 0.8422 (m110) REVERT: D 385 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8395 (pp) REVERT: F 355 ARG cc_start: 0.8262 (ttp-170) cc_final: 0.8027 (ptt180) REVERT: G 350 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: G 385 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8323 (pp) REVERT: J 246 ASN cc_start: 0.8364 (t0) cc_final: 0.7999 (t0) REVERT: K 385 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8369 (pp) REVERT: L 93 ASP cc_start: 0.8328 (t0) cc_final: 0.8040 (t0) outliers start: 85 outliers final: 63 residues processed: 496 average time/residue: 0.4894 time to fit residues: 390.2845 Evaluate side-chains 474 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 405 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 GLN Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 75 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 225 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN C 196 ASN K 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117713 restraints weight = 134421.004| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.93 r_work: 0.2968 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33312 Z= 0.115 Angle : 0.476 8.016 45324 Z= 0.236 Chirality : 0.044 0.137 5244 Planarity : 0.004 0.066 5904 Dihedral : 8.072 87.707 5174 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.75 % Allowed : 14.36 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.18 (0.12), residues: 4260 helix: 0.35 (0.12), residues: 1704 sheet: -0.87 (0.16), residues: 792 loop : 0.01 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 381 HIS 0.003 0.000 HIS L 124 PHE 0.008 0.001 PHE L 121 TYR 0.023 0.001 TYR C 361 ARG 0.004 0.000 ARG I 180 Details of bonding type rmsd hydrogen bonds : bond 0.02502 ( 1693) hydrogen bonds : angle 5.12811 ( 4611) covalent geometry : bond 0.00271 (33288) covalent geometry : angle 0.47648 (45324) Misc. bond : bond 0.00129 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 425 time to evaluate : 3.764 Fit side-chains REVERT: B 385 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.7960 (pp) REVERT: C 385 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.7950 (pp) REVERT: D 97 ASN cc_start: 0.8670 (m110) cc_final: 0.8405 (m110) REVERT: D 274 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8520 (tmtt) REVERT: D 385 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8445 (pp) REVERT: F 355 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7869 (ptt180) REVERT: G 350 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: G 385 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8305 (pp) REVERT: H 62 ILE cc_start: 0.8809 (mm) cc_final: 0.8592 (mt) REVERT: I 62 ILE cc_start: 0.8762 (mm) cc_final: 0.8530 (mt) REVERT: I 251 LEU cc_start: 0.8776 (tp) cc_final: 0.8487 (tp) REVERT: J 246 ASN cc_start: 0.8340 (t0) cc_final: 0.7986 (t0) REVERT: K 385 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8318 (pp) REVERT: L 93 ASP cc_start: 0.8344 (t0) cc_final: 0.8074 (t0) outliers start: 82 outliers final: 62 residues processed: 483 average time/residue: 0.6011 time to fit residues: 477.2785 Evaluate side-chains 468 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 400 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 274 LYS Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 291 optimal weight: 0.8980 chunk 387 optimal weight: 0.0070 chunk 231 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 246 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 402 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN D 196 ASN H 196 ASN I 97 ASN K 323 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117844 restraints weight = 145058.354| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.17 r_work: 0.2950 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33312 Z= 0.109 Angle : 0.471 8.765 45324 Z= 0.232 Chirality : 0.044 0.139 5244 Planarity : 0.004 0.062 5904 Dihedral : 7.846 81.469 5168 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.60 % Allowed : 14.47 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.02 (0.12), residues: 4260 helix: 0.55 (0.13), residues: 1704 sheet: -0.80 (0.16), residues: 792 loop : 0.09 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 381 HIS 0.002 0.000 HIS A 124 PHE 0.008 0.001 PHE H 121 TYR 0.025 0.001 TYR C 361 ARG 0.004 0.000 ARG F 242 Details of bonding type rmsd hydrogen bonds : bond 0.02453 ( 1693) hydrogen bonds : angle 5.04149 ( 4611) covalent geometry : bond 0.00256 (33288) covalent geometry : angle 0.47055 (45324) Misc. bond : bond 0.00120 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 414 time to evaluate : 3.310 Fit side-chains REVERT: B 385 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.7931 (pp) REVERT: C 385 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.7975 (pp) REVERT: D 86 ARG cc_start: 0.8652 (mtm180) cc_final: 0.8220 (mtm180) REVERT: D 107 MET cc_start: 0.8646 (mtp) cc_final: 0.8354 (ttt) REVERT: D 385 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8502 (pp) REVERT: G 102 ARG cc_start: 0.8685 (ttp-110) cc_final: 0.8350 (ttp-110) REVERT: G 385 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8337 (pp) REVERT: H 62 ILE cc_start: 0.8817 (mm) cc_final: 0.8613 (mt) REVERT: H 355 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8147 (ptt180) REVERT: I 62 ILE cc_start: 0.8810 (mm) cc_final: 0.8608 (mt) REVERT: I 251 LEU cc_start: 0.8783 (tp) cc_final: 0.8495 (tp) REVERT: J 62 ILE cc_start: 0.8861 (mm) cc_final: 0.8589 (mt) REVERT: J 246 ASN cc_start: 0.8366 (t0) cc_final: 0.8008 (t0) REVERT: K 385 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8355 (pp) REVERT: L 93 ASP cc_start: 0.8385 (t0) cc_final: 0.8108 (t0) outliers start: 77 outliers final: 59 residues processed: 471 average time/residue: 0.4563 time to fit residues: 348.0533 Evaluate side-chains 465 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 400 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 274 LYS Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 368 optimal weight: 0.6980 chunk 335 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN D 322 GLN E 196 ASN I 100 HIS L 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114539 restraints weight = 146422.510| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.16 r_work: 0.2576 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33312 Z= 0.148 Angle : 0.497 7.890 45324 Z= 0.244 Chirality : 0.045 0.138 5244 Planarity : 0.004 0.073 5904 Dihedral : 7.898 79.396 5164 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.66 % Allowed : 14.59 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.01 (0.12), residues: 4260 helix: 0.47 (0.12), residues: 1716 sheet: -0.85 (0.16), residues: 792 loop : 0.16 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 381 HIS 0.004 0.000 HIS H 109 PHE 0.008 0.001 PHE L 121 TYR 0.026 0.001 TYR C 361 ARG 0.004 0.000 ARG J 355 Details of bonding type rmsd hydrogen bonds : bond 0.02661 ( 1693) hydrogen bonds : angle 5.14519 ( 4611) covalent geometry : bond 0.00359 (33288) covalent geometry : angle 0.49734 (45324) Misc. bond : bond 0.00165 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 404 time to evaluate : 3.351 Fit side-chains REVERT: B 385 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7838 (pp) REVERT: C 385 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7727 (pp) REVERT: D 86 ARG cc_start: 0.8580 (mtm180) cc_final: 0.8141 (mtm180) REVERT: D 97 ASN cc_start: 0.8616 (m110) cc_final: 0.8362 (m110) REVERT: D 107 MET cc_start: 0.8602 (mtp) cc_final: 0.8355 (ttt) REVERT: D 385 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8267 (pp) REVERT: E 86 ARG cc_start: 0.8720 (mtm180) cc_final: 0.8364 (mtm180) REVERT: G 385 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8148 (pp) REVERT: H 62 ILE cc_start: 0.8689 (mm) cc_final: 0.8450 (mt) REVERT: H 355 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7960 (ptt180) REVERT: I 62 ILE cc_start: 0.8656 (mm) cc_final: 0.8418 (mt) REVERT: I 251 LEU cc_start: 0.8698 (tp) cc_final: 0.8412 (tp) REVERT: J 62 ILE cc_start: 0.8691 (mm) cc_final: 0.8401 (mt) REVERT: J 246 ASN cc_start: 0.8392 (t0) cc_final: 0.7989 (t0) REVERT: K 385 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8192 (pp) REVERT: L 93 ASP cc_start: 0.8328 (t0) cc_final: 0.7949 (t0) outliers start: 79 outliers final: 64 residues processed: 464 average time/residue: 0.4534 time to fit residues: 339.2561 Evaluate side-chains 455 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 385 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 97 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 229 optimal weight: 0.5980 chunk 324 optimal weight: 3.9990 chunk 348 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN E 196 ASN G 85 ASN H 196 ASN L 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116588 restraints weight = 143822.814| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.06 r_work: 0.2623 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33312 Z= 0.123 Angle : 0.481 7.736 45324 Z= 0.237 Chirality : 0.045 0.140 5244 Planarity : 0.004 0.068 5904 Dihedral : 7.833 78.817 5164 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.66 % Allowed : 14.39 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.14 (0.12), residues: 4260 helix: 0.67 (0.13), residues: 1704 sheet: -0.81 (0.16), residues: 792 loop : 0.18 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 381 HIS 0.002 0.000 HIS A 124 PHE 0.008 0.001 PHE L 121 TYR 0.027 0.001 TYR C 361 ARG 0.006 0.000 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 1693) hydrogen bonds : angle 5.06038 ( 4611) covalent geometry : bond 0.00291 (33288) covalent geometry : angle 0.48081 (45324) Misc. bond : bond 0.00135 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 390 time to evaluate : 3.968 Fit side-chains REVERT: B 62 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 385 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7800 (pp) REVERT: C 385 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7708 (pp) REVERT: D 97 ASN cc_start: 0.8588 (m110) cc_final: 0.8327 (m110) REVERT: D 107 MET cc_start: 0.8550 (mtp) cc_final: 0.8316 (ttt) REVERT: D 274 LYS cc_start: 0.8757 (tmtt) cc_final: 0.8495 (tmtt) REVERT: D 385 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8282 (pp) REVERT: E 62 ILE cc_start: 0.8597 (mm) cc_final: 0.8327 (mt) REVERT: E 86 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8344 (mtm180) REVERT: G 79 ASP cc_start: 0.8283 (m-30) cc_final: 0.8078 (m-30) REVERT: G 385 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8135 (pp) REVERT: H 62 ILE cc_start: 0.8667 (mm) cc_final: 0.8432 (mt) REVERT: H 355 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7782 (ptt180) REVERT: I 62 ILE cc_start: 0.8619 (mm) cc_final: 0.8387 (mt) REVERT: I 251 LEU cc_start: 0.8648 (tp) cc_final: 0.8434 (tp) REVERT: J 62 ILE cc_start: 0.8691 (mm) cc_final: 0.8425 (mt) REVERT: J 246 ASN cc_start: 0.8366 (t0) cc_final: 0.7972 (t0) REVERT: K 385 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8157 (pp) REVERT: L 93 ASP cc_start: 0.8283 (t0) cc_final: 0.7895 (t0) outliers start: 79 outliers final: 70 residues processed: 445 average time/residue: 0.4731 time to fit residues: 342.8873 Evaluate side-chains 454 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 377 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 26 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 123 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 HIS L 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114340 restraints weight = 151759.817| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.16 r_work: 0.2567 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 33312 Z= 0.159 Angle : 0.503 7.674 45324 Z= 0.247 Chirality : 0.045 0.139 5244 Planarity : 0.004 0.067 5904 Dihedral : 7.911 80.007 5164 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.75 % Allowed : 14.36 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.01 (0.12), residues: 4260 helix: 0.53 (0.12), residues: 1716 sheet: -0.99 (0.15), residues: 816 loop : 0.19 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 381 HIS 0.003 0.000 HIS I 109 PHE 0.008 0.001 PHE D 199 TYR 0.030 0.001 TYR D 361 ARG 0.006 0.000 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.02728 ( 1693) hydrogen bonds : angle 5.16462 ( 4611) covalent geometry : bond 0.00385 (33288) covalent geometry : angle 0.50342 (45324) Misc. bond : bond 0.00175 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 372 time to evaluate : 3.605 Fit side-chains REVERT: B 62 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8599 (mt) REVERT: B 385 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.7836 (pp) REVERT: C 385 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7722 (pp) REVERT: D 97 ASN cc_start: 0.8612 (m110) cc_final: 0.8343 (m110) REVERT: D 107 MET cc_start: 0.8558 (mtp) cc_final: 0.8351 (ttt) REVERT: D 274 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8537 (tmtt) REVERT: D 385 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8285 (pp) REVERT: E 86 ARG cc_start: 0.8714 (mtm180) cc_final: 0.8348 (mtm180) REVERT: G 385 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8158 (pp) REVERT: H 62 ILE cc_start: 0.8675 (mm) cc_final: 0.8443 (mt) REVERT: H 355 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7930 (ptt180) REVERT: I 62 ILE cc_start: 0.8648 (mm) cc_final: 0.8406 (mt) REVERT: I 251 LEU cc_start: 0.8694 (tp) cc_final: 0.8434 (tp) REVERT: J 62 ILE cc_start: 0.8673 (mm) cc_final: 0.8385 (mt) REVERT: J 246 ASN cc_start: 0.8408 (t0) cc_final: 0.8016 (t0) REVERT: K 246 ASN cc_start: 0.8152 (t0) cc_final: 0.7851 (t0) REVERT: K 385 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8189 (pp) REVERT: L 35 LYS cc_start: 0.7753 (pttm) cc_final: 0.7510 (pttm) REVERT: L 93 ASP cc_start: 0.8286 (t0) cc_final: 0.7906 (t0) outliers start: 82 outliers final: 71 residues processed: 432 average time/residue: 0.4513 time to fit residues: 321.3111 Evaluate side-chains 441 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 363 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 275 optimal weight: 0.7980 chunk 416 optimal weight: 0.5980 chunk 304 optimal weight: 0.7980 chunk 364 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 122 optimal weight: 0.0870 chunk 251 optimal weight: 4.9990 chunk 289 optimal weight: 0.3980 chunk 340 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN L 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117591 restraints weight = 150604.927| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.32 r_work: 0.3005 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 33312 Z= 0.106 Angle : 0.472 7.395 45324 Z= 0.233 Chirality : 0.044 0.141 5244 Planarity : 0.004 0.066 5904 Dihedral : 7.757 78.725 5164 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.57 % Allowed : 14.56 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.29 (0.12), residues: 4260 helix: 0.83 (0.13), residues: 1704 sheet: -0.74 (0.16), residues: 792 loop : 0.22 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 381 HIS 0.002 0.000 HIS A 124 PHE 0.007 0.001 PHE L 121 TYR 0.027 0.001 TYR C 361 ARG 0.005 0.000 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.02461 ( 1693) hydrogen bonds : angle 4.98526 ( 4611) covalent geometry : bond 0.00247 (33288) covalent geometry : angle 0.47250 (45324) Misc. bond : bond 0.00109 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17209.56 seconds wall clock time: 299 minutes 32.49 seconds (17972.49 seconds total)