Starting phenix.real_space_refine on Fri May 30 03:00:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2n_18852/05_2025/8r2n_18852_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2n_18852/05_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_18852/05_2025/8r2n_18852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2n_18852/05_2025/8r2n_18852.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2n_18852/05_2025/8r2n_18852_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2n_18852/05_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 34.96, per 1000 atoms: 1.05 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: 9.22 Conformation dependent library (CDL) restraints added in 8.7 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: 4.96 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: 14.04 Time building geometry restraints manager: 10.53 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: 3.650 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: 1.520 Check model and map are aligned: 0.250 Set scattering table: 0.340 Process input model: 99.880 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.260 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.280 ------------------------------------------------------------------------------- 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 : 3.591 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: 0.4363 time to fit residues: 354.7175 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 : 3.908 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113222 restraints weight = 144638.872| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.19 r_work: 0.2560 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 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 = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 89.676 5244 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.97 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 5.78368 ( 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 : 3.508 Fit side-chains REVERT: A 237 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: A 385 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8380 (pp) REVERT: B 385 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7796 (pp) REVERT: C 62 ILE cc_start: 0.8674 (mm) cc_final: 0.8473 (mm) REVERT: C 164 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: C 385 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7861 (pp) REVERT: D 97 ASN cc_start: 0.8595 (m110) cc_final: 0.8343 (m110) REVERT: D 107 MET cc_start: 0.8571 (mtp) cc_final: 0.8342 (ttt) REVERT: D 385 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8151 (pp) REVERT: E 355 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7849 (ptt180) REVERT: G 164 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8154 (m-30) REVERT: G 350 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: G 355 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7896 (ttp-110) REVERT: G 361 TYR cc_start: 0.9185 (p90) cc_final: 0.8958 (p90) REVERT: G 385 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8138 (pp) REVERT: I 62 ILE cc_start: 0.8720 (mm) cc_final: 0.8490 (mm) REVERT: I 89 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8636 (mt) REVERT: I 180 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7339 (ttm170) REVERT: J 246 ASN cc_start: 0.8337 (t0) cc_final: 0.7972 (t0) REVERT: K 385 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8168 (pp) REVERT: L 93 ASP cc_start: 0.8408 (t0) cc_final: 0.7977 (t0) outliers start: 92 outliers final: 60 residues processed: 516 average time/residue: 0.4670 time to fit residues: 385.7279 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 : 3.508 ------------------------------------------------------------------------------- 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: 0.9990 chunk 205 optimal weight: 2.9990 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: 3.9990 chunk 263 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.129386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111389 restraints weight = 136695.814| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.07 r_work: 0.2532 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 33312 Z= 0.191 Angle : 0.536 6.977 45324 Z= 0.265 Chirality : 0.046 0.136 5244 Planarity : 0.004 0.052 5904 Dihedral : 9.080 82.371 5204 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.19 % Allowed : 12.13 % Favored : 84.68 % 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: -1.29 (0.12), residues: 4260 helix: -0.67 (0.12), residues: 1692 sheet: -1.46 (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 0.001 HIS I 109 PHE 0.011 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 0.03003 ( 1693) hydrogen bonds : angle 5.67775 ( 4611) covalent geometry : bond 0.00465 (33288) covalent geometry : angle 0.53571 (45324) Misc. bond : bond 0.00219 ( 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 519 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 422 time to evaluate : 3.676 Fit side-chains REVERT: A 107 MET cc_start: 0.9228 (mmm) cc_final: 0.9007 (mmm) REVERT: A 237 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (mt0) REVERT: A 355 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7864 (ptt180) REVERT: B 385 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7890 (pp) REVERT: C 35 LYS cc_start: 0.8040 (pttp) cc_final: 0.7798 (pttm) REVERT: C 164 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: C 184 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7882 (mtm110) REVERT: C 385 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7846 (pp) REVERT: D 97 ASN cc_start: 0.8635 (m110) cc_final: 0.8383 (m110) REVERT: D 184 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8230 (ttp80) REVERT: D 385 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8205 (pp) REVERT: E 355 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7863 (ptt180) REVERT: G 164 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: G 350 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: G 379 ASN cc_start: 0.9191 (p0) cc_final: 0.8943 (p0) REVERT: G 385 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8258 (pp) REVERT: I 62 ILE cc_start: 0.8740 (mm) cc_final: 0.8498 (mm) REVERT: J 246 ASN cc_start: 0.8398 (t0) cc_final: 0.8030 (t0) REVERT: J 378 GLU cc_start: 0.8810 (tp30) cc_final: 0.8575 (tp30) REVERT: K 385 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8307 (pp) REVERT: L 93 ASP cc_start: 0.8354 (t0) cc_final: 0.7927 (t0) outliers start: 97 outliers final: 67 residues processed: 488 average time/residue: 0.4572 time to fit residues: 357.6834 Evaluate side-chains 465 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 389 time to evaluate : 3.894 ------------------------------------------------------------------------------- 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 A residue 237 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 73 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 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 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 206 THR 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 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 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 385 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 93 ASP 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 251 LEU 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 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 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: 1.9990 chunk 217 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 299 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN D 85 ASN G 85 ASN I 97 ASN J 109 HIS K 323 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113481 restraints weight = 159221.928| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.42 r_work: 0.2550 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1347 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= 0.147 Angle : 0.503 6.445 45324 Z= 0.249 Chirality : 0.045 0.132 5244 Planarity : 0.004 0.052 5904 Dihedral : 8.673 87.794 5189 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.16 % Allowed : 12.78 % Favored : 84.06 % 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: -0.91 (0.12), residues: 4260 helix: -0.30 (0.12), residues: 1692 sheet: -1.30 (0.15), residues: 816 loop : -0.29 (0.14), residues: 1752 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 J 355 Details of bonding type rmsd hydrogen bonds : bond 0.02720 ( 1693) hydrogen bonds : angle 5.47184 ( 4611) covalent geometry : bond 0.00354 (33288) covalent geometry : angle 0.50299 (45324) Misc. bond : bond 0.00168 ( 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 519 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 423 time to evaluate : 3.447 Fit side-chains REVERT: A 355 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7753 (ptt180) REVERT: B 385 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7810 (pp) REVERT: C 164 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: C 355 ARG cc_start: 0.7959 (ttp-110) cc_final: 0.7744 (ptt180) REVERT: C 385 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7801 (pp) REVERT: D 72 TYR cc_start: 0.9198 (m-80) cc_final: 0.8969 (m-80) REVERT: D 97 ASN cc_start: 0.8605 (m110) cc_final: 0.8359 (m110) REVERT: D 184 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8195 (ttp80) REVERT: D 385 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8173 (pp) REVERT: F 355 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7764 (ptt180) REVERT: G 164 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: G 350 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: G 379 ASN cc_start: 0.9172 (p0) cc_final: 0.8917 (p0) REVERT: G 385 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8207 (pp) REVERT: I 62 ILE cc_start: 0.8721 (mm) cc_final: 0.8510 (mm) REVERT: J 246 ASN cc_start: 0.8365 (t0) cc_final: 0.7987 (t0) REVERT: J 355 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7713 (ptt180) REVERT: K 385 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8241 (pp) REVERT: L 93 ASP cc_start: 0.8359 (t0) cc_final: 0.7877 (t0) REVERT: L 355 ARG cc_start: 0.8045 (ttp-110) cc_final: 0.7772 (ptt180) outliers start: 96 outliers final: 67 residues processed: 487 average time/residue: 0.4907 time to fit residues: 382.6616 Evaluate side-chains 475 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 400 time to evaluate : 3.660 ------------------------------------------------------------------------------- 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 251 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 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 206 THR Chi-restraints excluded: chain D residue 236 LEU 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 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 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 236 LEU 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 93 ASP 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: 2.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 229 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 378 optimal weight: 0.6980 chunk 245 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 361 optimal weight: 0.0000 chunk 353 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 B 85 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 = 0.3521 r_free = 0.3521 target = 0.131986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114556 restraints weight = 135742.801| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.94 r_work: 0.2591 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 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 = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33312 Z= 0.148 Angle : 0.498 6.393 45324 Z= 0.247 Chirality : 0.045 0.134 5244 Planarity : 0.004 0.064 5904 Dihedral : 8.540 89.638 5184 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.16 % Allowed : 13.39 % Favored : 83.45 % 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: -0.67 (0.12), residues: 4260 helix: -0.10 (0.12), residues: 1704 sheet: -1.19 (0.15), residues: 816 loop : -0.14 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 381 HIS 0.002 0.000 HIS L 124 PHE 0.009 0.001 PHE L 121 TYR 0.022 0.001 TYR C 361 ARG 0.006 0.000 ARG G 355 Details of bonding type rmsd hydrogen bonds : bond 0.02696 ( 1693) hydrogen bonds : angle 5.39481 ( 4611) covalent geometry : bond 0.00357 (33288) covalent geometry : angle 0.49817 (45324) Misc. bond : bond 0.00171 ( 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: 96 poor density : 426 time to evaluate : 3.485 Fit side-chains REVERT: A 355 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7762 (ptt180) REVERT: B 385 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.7841 (pp) REVERT: C 164 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: C 385 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7811 (pp) REVERT: D 72 TYR cc_start: 0.9229 (m-80) cc_final: 0.9018 (m-80) REVERT: D 97 ASN cc_start: 0.8610 (m110) cc_final: 0.8353 (m110) REVERT: D 385 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8218 (pp) REVERT: F 355 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.7781 (ptt180) REVERT: G 164 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: G 355 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.7765 (ptt180) REVERT: G 379 ASN cc_start: 0.9167 (p0) cc_final: 0.8927 (p0) REVERT: G 385 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8237 (pp) REVERT: J 246 ASN cc_start: 0.8369 (t0) cc_final: 0.7978 (t0) REVERT: K 385 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8274 (pp) REVERT: L 355 ARG cc_start: 0.8024 (ttp-110) cc_final: 0.7817 (ptt180) outliers start: 96 outliers final: 73 residues processed: 489 average time/residue: 0.4625 time to fit residues: 359.2399 Evaluate side-chains 475 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 3.648 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 93 ASP 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 77 ILE 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 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 206 THR Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU 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 F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 251 LEU 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 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 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 236 LEU 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 89 LEU Chi-restraints excluded: chain K residue 93 ASP 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 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: 3.9990 chunk 141 optimal weight: 3.9990 chunk 108 optimal weight: 0.0870 chunk 111 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 195 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 225 optimal weight: 0.1980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 I 97 ASN K 323 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118783 restraints weight = 134367.156| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.93 r_work: 0.2990 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- 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 = 0.27 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 = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33312 Z= 0.099 Angle : 0.468 5.760 45324 Z= 0.233 Chirality : 0.044 0.136 5244 Planarity : 0.004 0.059 5904 Dihedral : 8.160 80.230 5181 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.75 % Allowed : 14.18 % Favored : 83.07 % 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: -0.24 (0.12), residues: 4260 helix: 0.30 (0.12), residues: 1704 sheet: -0.93 (0.15), residues: 792 loop : -0.02 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 381 HIS 0.003 0.000 HIS A 124 PHE 0.009 0.001 PHE I 121 TYR 0.024 0.001 TYR C 361 ARG 0.006 0.000 ARG G 355 Details of bonding type rmsd hydrogen bonds : bond 0.02425 ( 1693) hydrogen bonds : angle 5.12923 ( 4611) covalent geometry : bond 0.00226 (33288) covalent geometry : angle 0.46794 (45324) Misc. bond : bond 0.00107 ( 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 533 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 451 time to evaluate : 3.515 Fit side-chains REVERT: B 385 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.7938 (pp) REVERT: C 385 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.7962 (pp) REVERT: D 97 ASN cc_start: 0.8639 (m110) cc_final: 0.8382 (m110) REVERT: D 385 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8411 (pp) REVERT: F 120 ASP cc_start: 0.8803 (m-30) cc_final: 0.8280 (m-30) REVERT: F 355 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7892 (ptt180) REVERT: G 385 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8289 (pp) REVERT: H 62 ILE cc_start: 0.8757 (mm) cc_final: 0.8554 (mt) REVERT: I 251 LEU cc_start: 0.8749 (tp) cc_final: 0.8433 (tp) REVERT: J 246 ASN cc_start: 0.8341 (t0) cc_final: 0.7955 (t0) REVERT: K 385 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8315 (pp) outliers start: 82 outliers final: 52 residues processed: 511 average time/residue: 0.4641 time to fit residues: 383.0346 Evaluate side-chains 462 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 3.649 ------------------------------------------------------------------------------- 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 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 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 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 191 ILE 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 G residue 47 LYS 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 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 75 GLU Chi-restraints excluded: chain I residue 164 ASP 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 237 GLN Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 291 optimal weight: 0.9990 chunk 387 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 365 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 186 optimal weight: 0.5980 chunk 402 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 K 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115584 restraints weight = 145518.607| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.16 r_work: 0.2582 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1675 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= 0.144 Angle : 0.498 8.577 45324 Z= 0.244 Chirality : 0.045 0.134 5244 Planarity : 0.005 0.069 5904 Dihedral : 8.080 78.912 5170 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.89 % Allowed : 14.24 % 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: -0.20 (0.12), residues: 4260 helix: 0.39 (0.12), residues: 1704 sheet: -1.04 (0.15), residues: 816 loop : 0.04 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 381 HIS 0.002 0.000 HIS L 124 PHE 0.008 0.001 PHE L 121 TYR 0.025 0.001 TYR C 361 ARG 0.005 0.000 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.02624 ( 1693) hydrogen bonds : angle 5.19112 ( 4611) covalent geometry : bond 0.00348 (33288) covalent geometry : angle 0.49794 (45324) Misc. bond : bond 0.00162 ( 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 502 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 415 time to evaluate : 3.649 Fit side-chains REVERT: B 385 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7822 (pp) REVERT: C 385 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7805 (pp) REVERT: D 97 ASN cc_start: 0.8622 (m110) cc_final: 0.8364 (m110) REVERT: D 107 MET cc_start: 0.8591 (mtp) cc_final: 0.8311 (ttt) REVERT: D 385 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8231 (pp) REVERT: F 355 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7855 (ptt180) REVERT: G 385 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8173 (pp) REVERT: H 62 ILE cc_start: 0.8657 (mm) cc_final: 0.8426 (mt) REVERT: H 355 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7987 (ptt180) REVERT: I 62 ILE cc_start: 0.8626 (mm) cc_final: 0.8362 (mt) REVERT: J 246 ASN cc_start: 0.8381 (t0) cc_final: 0.7969 (t0) REVERT: K 385 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8201 (pp) outliers start: 87 outliers final: 68 residues processed: 481 average time/residue: 0.4489 time to fit residues: 345.7877 Evaluate side-chains 471 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 397 time to evaluate : 3.445 ------------------------------------------------------------------------------- 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 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 236 LEU 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 66 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 251 LEU 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 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 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 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 104 VAL Chi-restraints excluded: chain J residue 164 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 126 optimal weight: 0.0670 chunk 368 optimal weight: 0.9980 chunk 335 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117048 restraints weight = 146654.545| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.13 r_work: 0.2653 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33312 Z= 0.121 Angle : 0.483 8.715 45324 Z= 0.238 Chirality : 0.045 0.138 5244 Planarity : 0.005 0.066 5904 Dihedral : 7.998 79.006 5169 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.49 % Allowed : 14.80 % Favored : 82.72 % 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: -0.05 (0.12), residues: 4260 helix: 0.56 (0.12), residues: 1704 sheet: -1.00 (0.15), residues: 816 loop : 0.08 (0.14), residues: 1740 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 0.007 0.001 PHE L 121 TYR 0.027 0.001 TYR C 361 ARG 0.004 0.000 ARG I 180 Details of bonding type rmsd hydrogen bonds : bond 0.02523 ( 1693) hydrogen bonds : angle 5.10338 ( 4611) covalent geometry : bond 0.00287 (33288) covalent geometry : angle 0.48334 (45324) Misc. bond : bond 0.00139 ( 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 479 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 406 time to evaluate : 3.561 Fit side-chains REVERT: B 385 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7796 (pp) REVERT: C 62 ILE cc_start: 0.8567 (mm) cc_final: 0.8325 (mt) REVERT: C 184 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7537 (ttm170) REVERT: C 385 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7772 (pp) REVERT: D 97 ASN cc_start: 0.8586 (m110) cc_final: 0.8327 (m110) REVERT: D 107 MET cc_start: 0.8564 (mtp) cc_final: 0.8319 (ttt) REVERT: D 274 LYS cc_start: 0.8810 (tmtt) cc_final: 0.8540 (tmtt) REVERT: D 385 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8228 (pp) REVERT: F 355 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7865 (ptt180) REVERT: G 385 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8127 (pp) REVERT: H 355 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7791 (ptt180) REVERT: I 62 ILE cc_start: 0.8616 (mm) cc_final: 0.8362 (mt) REVERT: I 251 LEU cc_start: 0.8652 (tp) cc_final: 0.8385 (tp) REVERT: J 62 ILE cc_start: 0.8680 (mm) cc_final: 0.8389 (mt) REVERT: J 246 ASN cc_start: 0.8371 (t0) cc_final: 0.7958 (t0) REVERT: K 385 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8149 (pp) outliers start: 73 outliers final: 63 residues processed: 461 average time/residue: 0.4590 time to fit residues: 341.2160 Evaluate side-chains 463 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 394 time to evaluate : 3.648 ------------------------------------------------------------------------------- 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 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 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 236 LEU 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 97 optimal weight: 0.9990 chunk 149 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 229 optimal weight: 0.6980 chunk 324 optimal weight: 3.9990 chunk 348 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117800 restraints weight = 143884.275| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.19 r_work: 0.2956 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33312 Z= 0.105 Angle : 0.469 7.551 45324 Z= 0.232 Chirality : 0.044 0.142 5244 Planarity : 0.004 0.063 5904 Dihedral : 7.771 79.266 5165 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.60 % Allowed : 14.62 % Favored : 82.78 % 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: 0.20 (0.12), residues: 4260 helix: 0.76 (0.13), residues: 1704 sheet: -0.79 (0.16), residues: 792 loop : 0.17 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 381 HIS 0.003 0.000 HIS B 109 PHE 0.009 0.001 PHE L 121 TYR 0.027 0.001 TYR C 361 ARG 0.004 0.000 ARG L 355 Details of bonding type rmsd hydrogen bonds : bond 0.02422 ( 1693) hydrogen bonds : angle 4.98238 ( 4611) covalent geometry : bond 0.00244 (33288) covalent geometry : angle 0.46919 (45324) Misc. bond : bond 0.00115 ( 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 484 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 407 time to evaluate : 3.699 Fit side-chains REVERT: B 62 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8758 (mt) REVERT: B 385 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.7980 (pp) REVERT: C 184 ARG cc_start: 0.8195 (mtm110) cc_final: 0.7898 (ttm170) REVERT: C 385 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.7976 (pp) REVERT: D 86 ARG cc_start: 0.8807 (mtm180) cc_final: 0.8451 (mtm180) REVERT: D 107 MET cc_start: 0.8674 (mtp) cc_final: 0.8422 (ttt) REVERT: D 274 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8560 (tmtt) REVERT: D 385 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8505 (pp) REVERT: E 62 ILE cc_start: 0.8732 (mm) cc_final: 0.8512 (mt) REVERT: E 86 ARG cc_start: 0.8777 (mtm180) cc_final: 0.8491 (mtm180) REVERT: G 385 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8334 (pp) REVERT: H 355 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8155 (ptt180) REVERT: I 251 LEU cc_start: 0.8764 (tp) cc_final: 0.8519 (tp) REVERT: J 62 ILE cc_start: 0.8881 (mm) cc_final: 0.8662 (mt) REVERT: J 246 ASN cc_start: 0.8370 (t0) cc_final: 0.8028 (t0) REVERT: K 385 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8262 (pp) outliers start: 77 outliers final: 64 residues processed: 463 average time/residue: 0.4459 time to fit residues: 332.2193 Evaluate side-chains 458 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 387 time to evaluate : 3.416 ------------------------------------------------------------------------------- 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 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 385 LEU Chi-restraints excluded: chain C residue 47 LYS 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 236 LEU 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 66 VAL 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 F residue 251 LEU 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 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 75 GLU Chi-restraints excluded: chain I residue 104 VAL 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 89 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 164 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 26 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 123 optimal weight: 0.1980 chunk 344 optimal weight: 3.9990 chunk 298 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 297 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- 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 B 109 HIS B 196 ASN C 196 ASN D 196 ASN H 196 ASN L 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119041 restraints weight = 151811.450| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.39 r_work: 0.2957 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2030 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= 0.099 Angle : 0.464 7.474 45324 Z= 0.230 Chirality : 0.044 0.145 5244 Planarity : 0.005 0.074 5904 Dihedral : 7.684 80.410 5163 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.28 % Allowed : 15.03 % Favored : 82.69 % 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: 0.32 (0.12), residues: 4260 helix: 0.86 (0.13), residues: 1716 sheet: -0.82 (0.15), residues: 840 loop : 0.34 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 381 HIS 0.002 0.000 HIS A 124 PHE 0.008 0.001 PHE L 121 TYR 0.029 0.001 TYR D 361 ARG 0.006 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.02377 ( 1693) hydrogen bonds : angle 4.90223 ( 4611) covalent geometry : bond 0.00229 (33288) covalent geometry : angle 0.46448 (45324) Misc. bond : bond 0.00105 ( 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 476 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 410 time to evaluate : 3.646 Fit side-chains REVERT: A 62 ILE cc_start: 0.8710 (mm) cc_final: 0.8428 (mt) REVERT: B 62 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8712 (mt) REVERT: B 385 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.7954 (pp) REVERT: C 184 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7858 (ttm170) REVERT: C 385 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.7922 (pp) REVERT: D 107 MET cc_start: 0.8684 (mtp) cc_final: 0.8426 (ttt) REVERT: D 274 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8571 (tmtt) REVERT: D 385 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8525 (pp) REVERT: F 62 ILE cc_start: 0.8811 (mm) cc_final: 0.8580 (mt) REVERT: F 323 ASN cc_start: 0.8802 (m110) cc_final: 0.8496 (m110) REVERT: G 102 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8363 (ttp-110) REVERT: G 385 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8284 (pp) REVERT: I 251 LEU cc_start: 0.8751 (tp) cc_final: 0.8518 (tp) REVERT: J 246 ASN cc_start: 0.8358 (t0) cc_final: 0.8017 (t0) REVERT: K 62 ILE cc_start: 0.8795 (mm) cc_final: 0.8538 (mt) REVERT: K 385 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8368 (pp) outliers start: 66 outliers final: 56 residues processed: 459 average time/residue: 0.4261 time to fit residues: 321.5550 Evaluate side-chains 448 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 386 time to evaluate : 3.604 ------------------------------------------------------------------------------- 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 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 385 LEU Chi-restraints excluded: chain C residue 47 LYS 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 385 LEU Chi-restraints excluded: chain D residue 47 LYS 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 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 66 VAL 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 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 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 164 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 275 optimal weight: 0.9990 chunk 416 optimal weight: 1.9990 chunk 304 optimal weight: 0.9980 chunk 364 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 340 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 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 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN I 109 HIS J 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117392 restraints weight = 151129.504| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.34 r_work: 0.2605 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33312 Z= 0.128 Angle : 0.485 8.083 45324 Z= 0.238 Chirality : 0.045 0.142 5244 Planarity : 0.005 0.071 5904 Dihedral : 7.730 81.632 5162 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.49 % Allowed : 14.80 % Favored : 82.72 % 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: 0.31 (0.12), residues: 4260 helix: 0.80 (0.13), residues: 1716 sheet: -0.73 (0.16), residues: 792 loop : 0.27 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 381 HIS 0.003 0.000 HIS H 109 PHE 0.008 0.001 PHE L 121 TYR 0.027 0.001 TYR D 361 ARG 0.006 0.000 ARG J 355 Details of bonding type rmsd hydrogen bonds : bond 0.02539 ( 1693) hydrogen bonds : angle 4.97610 ( 4611) covalent geometry : bond 0.00305 (33288) covalent geometry : angle 0.48518 (45324) Misc. bond : bond 0.00144 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15944.33 seconds wall clock time: 276 minutes 50.81 seconds (16610.81 seconds total)