Starting phenix.real_space_refine on Tue Aug 26 03:21:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2n_18852/08_2025/8r2n_18852_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2n_18852/08_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_18852/08_2025/8r2n_18852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2n_18852/08_2025/8r2n_18852.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2n_18852/08_2025/8r2n_18852_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2n_18852/08_2025/8r2n_18852_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 12.29, per 1000 atoms: 0.37 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: 2.22 Conformation dependent library (CDL) restraints added in 2.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.23 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: 5.66 Time building geometry restraints manager: 2.90 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: 0.01 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 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 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 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 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 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 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 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 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 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 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 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 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 33.980 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.010 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG G 119 TYR 0.007 0.001 TYR H 263 PHE 0.013 0.001 PHE E 121 TRP 0.004 0.001 TRP E 381 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00504 (33288) covalent geometry : angle 0.77902 (45324) hydrogen bonds : bond 0.15716 ( 1693) hydrogen bonds : angle 7.61175 ( 4611) 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 : 1.176 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: 0.1862 time to fit residues: 153.4728 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 : 1.183 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN 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 J 322 GLN L 85 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114216 restraints weight = 133798.194| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.07 r_work: 0.2579 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33312 Z= 0.137 Angle : 0.524 6.689 45324 Z= 0.262 Chirality : 0.045 0.145 5244 Planarity : 0.005 0.059 5904 Dihedral : 9.476 89.742 5244 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.10 % Allowed : 11.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.12), residues: 4260 helix: -1.00 (0.12), residues: 1692 sheet: -1.46 (0.15), residues: 792 loop : -0.70 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 355 TYR 0.016 0.001 TYR C 361 PHE 0.015 0.001 PHE I 121 TRP 0.006 0.001 TRP E 381 HIS 0.002 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00324 (33288) covalent geometry : angle 0.52366 (45324) hydrogen bonds : bond 0.02958 ( 1693) hydrogen bonds : angle 5.75655 ( 4611) Misc. bond : bond 0.00146 ( 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 550 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 456 time to evaluate : 0.882 Fit side-chains REVERT: A 237 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: B 385 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.7810 (pp) REVERT: C 164 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: C 385 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7891 (pp) REVERT: D 97 ASN cc_start: 0.8627 (m110) cc_final: 0.8366 (m110) REVERT: D 107 MET cc_start: 0.8558 (mtp) cc_final: 0.8346 (ttt) REVERT: D 274 LYS cc_start: 0.8855 (tmtt) cc_final: 0.8655 (tmtt) REVERT: D 385 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8172 (pp) REVERT: F 120 ASP cc_start: 0.8792 (m-30) cc_final: 0.8188 (m-30) REVERT: F 233 ASP cc_start: 0.7867 (m-30) cc_final: 0.7665 (m-30) REVERT: G 164 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: G 350 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: G 355 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7931 (ttp-110) REVERT: G 361 TYR cc_start: 0.9198 (p90) cc_final: 0.8926 (p90) REVERT: G 385 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8192 (pp) REVERT: I 62 ILE cc_start: 0.8743 (mm) cc_final: 0.8520 (mm) REVERT: I 251 LEU cc_start: 0.8720 (tp) cc_final: 0.8428 (tp) REVERT: J 246 ASN cc_start: 0.8327 (t0) cc_final: 0.7971 (t0) REVERT: K 385 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8234 (pp) REVERT: L 93 ASP cc_start: 0.8406 (t0) cc_final: 0.7980 (t0) outliers start: 94 outliers final: 61 residues processed: 524 average time/residue: 0.2004 time to fit residues: 168.1900 Evaluate side-chains 484 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 414 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 79 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 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 194 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 104 VAL 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 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 129 optimal weight: 5.9990 chunk 419 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 chunk 413 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 291 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 137 optimal weight: 0.1980 chunk 407 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 D 85 ASN G 85 ASN I 97 ASN I 109 HIS K 196 ASN K 323 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117003 restraints weight = 144524.226| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.12 r_work: 0.2612 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33312 Z= 0.116 Angle : 0.486 6.196 45324 Z= 0.242 Chirality : 0.044 0.134 5244 Planarity : 0.004 0.052 5904 Dihedral : 8.730 82.677 5198 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.69 % Allowed : 12.57 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.12), residues: 4260 helix: -0.41 (0.12), residues: 1692 sheet: -1.21 (0.15), residues: 792 loop : -0.44 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 355 TYR 0.014 0.001 TYR G 361 PHE 0.013 0.001 PHE I 121 TRP 0.005 0.001 TRP E 381 HIS 0.003 0.000 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00274 (33288) covalent geometry : angle 0.48626 (45324) hydrogen bonds : bond 0.02652 ( 1693) hydrogen bonds : angle 5.41125 ( 4611) Misc. bond : bond 0.00135 ( 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 549 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 469 time to evaluate : 0.951 Fit side-chains REVERT: A 107 MET cc_start: 0.9181 (mmm) cc_final: 0.8937 (mmm) REVERT: B 385 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7786 (pp) REVERT: C 164 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: C 184 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7864 (mtm110) REVERT: C 385 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7858 (pp) REVERT: D 97 ASN cc_start: 0.8606 (m110) cc_final: 0.8341 (m110) REVERT: D 184 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8194 (ttp80) REVERT: D 274 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8520 (tmtt) REVERT: D 385 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8223 (pp) REVERT: F 120 ASP cc_start: 0.8772 (m-30) cc_final: 0.8160 (m-30) REVERT: F 355 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7793 (ptt180) REVERT: G 350 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: G 379 ASN cc_start: 0.9176 (p0) cc_final: 0.8923 (p0) REVERT: G 385 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8157 (pp) REVERT: I 62 ILE cc_start: 0.8746 (mm) cc_final: 0.8537 (mm) REVERT: I 251 LEU cc_start: 0.8685 (tp) cc_final: 0.8403 (tp) REVERT: J 246 ASN cc_start: 0.8309 (t0) cc_final: 0.7943 (t0) REVERT: K 385 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8232 (pp) REVERT: L 93 ASP cc_start: 0.8295 (t0) cc_final: 0.7935 (t0) outliers start: 80 outliers final: 46 residues processed: 527 average time/residue: 0.1921 time to fit residues: 163.6633 Evaluate side-chains 471 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 418 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 191 ILE 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 F residue 47 LYS Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 350 GLU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 GLN Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS 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 374 optimal weight: 4.9990 chunk 285 optimal weight: 0.3980 chunk 237 optimal weight: 0.6980 chunk 223 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 50 optimal weight: 0.0070 chunk 25 optimal weight: 0.9980 chunk 300 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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** B 85 ASN B 109 HIS I 109 HIS K 323 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117902 restraints weight = 133793.428| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.00 r_work: 0.3097 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33312 Z= 0.114 Angle : 0.480 5.996 45324 Z= 0.238 Chirality : 0.044 0.147 5244 Planarity : 0.004 0.062 5904 Dihedral : 8.170 84.018 5175 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.78 % Allowed : 13.57 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.12), residues: 4260 helix: -0.07 (0.12), residues: 1704 sheet: -1.03 (0.15), residues: 792 loop : -0.24 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 355 TYR 0.020 0.001 TYR C 361 PHE 0.010 0.001 PHE H 121 TRP 0.004 0.001 TRP E 381 HIS 0.003 0.000 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00268 (33288) covalent geometry : angle 0.47996 (45324) hydrogen bonds : bond 0.02538 ( 1693) hydrogen bonds : angle 5.24386 ( 4611) Misc. bond : bond 0.00132 ( 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 535 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 452 time to evaluate : 0.994 Fit side-chains REVERT: B 385 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.7973 (pp) REVERT: C 184 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8104 (mtp180) REVERT: C 385 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8010 (pp) REVERT: D 97 ASN cc_start: 0.8686 (m110) cc_final: 0.8420 (m110) REVERT: D 274 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8556 (tmtt) REVERT: D 385 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8474 (pp) REVERT: G 350 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: G 379 ASN cc_start: 0.9257 (p0) cc_final: 0.9003 (p0) REVERT: G 385 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8316 (pp) REVERT: I 251 LEU cc_start: 0.8812 (tp) cc_final: 0.8510 (tp) REVERT: J 246 ASN cc_start: 0.8343 (t0) cc_final: 0.8008 (t0) REVERT: K 385 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8404 (pp) REVERT: L 93 ASP cc_start: 0.8391 (t0) cc_final: 0.8129 (t0) outliers start: 83 outliers final: 60 residues processed: 508 average time/residue: 0.1972 time to fit residues: 160.9457 Evaluate side-chains 483 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 417 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 385 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 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 73 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 191 ILE 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 75 GLU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 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 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 164 ASP 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 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 148 THR 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 171 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 417 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 261 optimal weight: 0.5980 chunk 338 optimal weight: 5.9990 chunk 399 optimal weight: 0.5980 chunk 346 optimal weight: 0.9990 chunk 309 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 85 ASN C 196 ASN I 97 ASN K 196 ASN K 323 ASN L 100 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116776 restraints weight = 126317.859| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.95 r_work: 0.2626 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1684 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= 0.122 Angle : 0.481 8.216 45324 Z= 0.238 Chirality : 0.044 0.144 5244 Planarity : 0.004 0.063 5904 Dihedral : 8.032 83.978 5170 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.87 % Allowed : 13.95 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.12), residues: 4260 helix: 0.18 (0.12), residues: 1704 sheet: -1.00 (0.16), residues: 804 loop : -0.04 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.022 0.001 TYR C 361 PHE 0.009 0.001 PHE H 121 TRP 0.004 0.001 TRP E 381 HIS 0.002 0.000 HIS L 124 Details of bonding type rmsd covalent geometry : bond 0.00291 (33288) covalent geometry : angle 0.48105 (45324) hydrogen bonds : bond 0.02556 ( 1693) hydrogen bonds : angle 5.16651 ( 4611) Misc. bond : bond 0.00142 ( 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 515 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 429 time to evaluate : 1.055 Fit side-chains REVERT: B 385 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.7757 (pp) REVERT: C 385 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7766 (pp) REVERT: D 97 ASN cc_start: 0.8567 (m110) cc_final: 0.8308 (m110) REVERT: D 385 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8226 (pp) REVERT: F 107 MET cc_start: 0.9120 (mmm) cc_final: 0.8881 (mmm) REVERT: G 350 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: G 385 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8095 (pp) REVERT: J 246 ASN cc_start: 0.8318 (t0) cc_final: 0.7942 (t0) REVERT: K 385 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8173 (pp) REVERT: L 93 ASP cc_start: 0.8273 (t0) cc_final: 0.7916 (t0) outliers start: 86 outliers final: 63 residues processed: 488 average time/residue: 0.1968 time to fit residues: 155.6653 Evaluate side-chains 471 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 402 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU 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 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 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 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 350 GLU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 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 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 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 148 THR 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 192 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 409 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN C 196 ASN K 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.112839 restraints weight = 146310.346| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.10 r_work: 0.2573 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33312 Z= 0.181 Angle : 0.522 9.447 45324 Z= 0.256 Chirality : 0.046 0.144 5244 Planarity : 0.004 0.060 5904 Dihedral : 8.090 87.070 5166 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.10 % Allowed : 13.71 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.12), residues: 4260 helix: 0.12 (0.12), residues: 1704 sheet: -1.10 (0.15), residues: 816 loop : -0.02 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 355 TYR 0.023 0.001 TYR C 361 PHE 0.008 0.001 PHE D 199 TRP 0.005 0.001 TRP G 381 HIS 0.002 0.000 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00440 (33288) covalent geometry : angle 0.52172 (45324) hydrogen bonds : bond 0.02859 ( 1693) hydrogen bonds : angle 5.34529 ( 4611) Misc. bond : bond 0.00199 ( 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 496 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 402 time to evaluate : 1.125 Fit side-chains REVERT: B 385 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.7879 (pp) REVERT: C 385 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7794 (pp) REVERT: D 72 TYR cc_start: 0.9280 (m-80) cc_final: 0.9036 (m-80) REVERT: D 97 ASN cc_start: 0.8615 (m110) cc_final: 0.8355 (m110) REVERT: D 274 LYS cc_start: 0.8827 (tmtt) cc_final: 0.8565 (tmtt) REVERT: D 385 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8238 (pp) REVERT: F 107 MET cc_start: 0.9145 (mmm) cc_final: 0.8930 (mmm) REVERT: G 355 ARG cc_start: 0.8600 (ptt180) cc_final: 0.8368 (ptt-90) REVERT: G 385 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8210 (pp) REVERT: J 246 ASN cc_start: 0.8395 (t0) cc_final: 0.8007 (t0) REVERT: K 385 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8260 (pp) REVERT: L 35 LYS cc_start: 0.7775 (pttm) cc_final: 0.7545 (pttm) REVERT: L 93 ASP cc_start: 0.8302 (t0) cc_final: 0.7911 (t0) outliers start: 94 outliers final: 68 residues processed: 465 average time/residue: 0.1925 time to fit residues: 144.7609 Evaluate side-chains 456 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 383 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 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 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 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 93 ASP 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 73 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 164 ASP 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 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 164 ASP Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 237 GLN Chi-restraints excluded: chain L residue 385 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 38 optimal weight: 0.5980 chunk 193 optimal weight: 0.8980 chunk 404 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 374 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 334 optimal weight: 0.5980 chunk 361 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN D 196 ASN I 100 HIS I 109 HIS L 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118282 restraints weight = 135608.761| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.97 r_work: 0.2644 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 33312 Z= 0.105 Angle : 0.474 7.613 45324 Z= 0.234 Chirality : 0.044 0.143 5244 Planarity : 0.004 0.055 5904 Dihedral : 7.895 85.632 5165 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.72 % Allowed : 14.36 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.12), residues: 4260 helix: 0.49 (0.13), residues: 1704 sheet: -0.84 (0.16), residues: 792 loop : 0.10 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 242 TYR 0.026 0.001 TYR C 361 PHE 0.008 0.001 PHE H 121 TRP 0.002 0.000 TRP C 381 HIS 0.002 0.000 HIS I 109 Details of bonding type rmsd covalent geometry : bond 0.00245 (33288) covalent geometry : angle 0.47420 (45324) hydrogen bonds : bond 0.02472 ( 1693) hydrogen bonds : angle 5.07461 ( 4611) Misc. bond : bond 0.00110 ( 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 494 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 413 time to evaluate : 1.359 Fit side-chains REVERT: B 385 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7785 (pp) REVERT: C 62 ILE cc_start: 0.8627 (mm) cc_final: 0.8384 (mt) REVERT: C 385 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7810 (pp) REVERT: D 72 TYR cc_start: 0.9189 (m-80) cc_final: 0.8921 (m-80) REVERT: D 97 ASN cc_start: 0.8589 (m110) cc_final: 0.8338 (m110) REVERT: D 107 MET cc_start: 0.8511 (mtp) cc_final: 0.8204 (ttt) REVERT: D 274 LYS cc_start: 0.8751 (tmtt) cc_final: 0.8493 (tmtt) REVERT: D 385 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8293 (pp) REVERT: F 107 MET cc_start: 0.9095 (mmm) cc_final: 0.8891 (mmm) REVERT: G 385 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8108 (pp) REVERT: H 62 ILE cc_start: 0.8682 (mm) cc_final: 0.8448 (mt) REVERT: H 355 ARG cc_start: 0.8326 (ttp-170) cc_final: 0.7834 (ptt180) REVERT: I 62 ILE cc_start: 0.8609 (mm) cc_final: 0.8367 (mt) REVERT: I 251 LEU cc_start: 0.8671 (tp) cc_final: 0.8414 (tp) REVERT: J 179 TYR cc_start: 0.9059 (t80) cc_final: 0.8746 (t80) REVERT: J 246 ASN cc_start: 0.8325 (t0) cc_final: 0.7920 (t0) REVERT: K 385 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8209 (pp) REVERT: L 93 ASP cc_start: 0.8270 (t0) cc_final: 0.7890 (t0) outliers start: 81 outliers final: 63 residues processed: 473 average time/residue: 0.1905 time to fit residues: 147.3462 Evaluate side-chains 465 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 397 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 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 89 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 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 385 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 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 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 164 ASP 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 236 LEU 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 236 LEU Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 148 THR 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 235 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 196 optimal weight: 0.0000 chunk 73 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 299 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 109 HIS I 109 HIS 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 = 0.135259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117489 restraints weight = 145552.238| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.17 r_work: 0.2997 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 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 = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1843 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= 0.114 Angle : 0.476 7.463 45324 Z= 0.234 Chirality : 0.044 0.144 5244 Planarity : 0.004 0.072 5904 Dihedral : 7.850 85.946 5165 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.60 % Allowed : 14.39 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.12), residues: 4260 helix: 0.64 (0.13), residues: 1704 sheet: -0.79 (0.16), residues: 792 loop : 0.16 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 355 TYR 0.026 0.001 TYR C 361 PHE 0.007 0.001 PHE L 121 TRP 0.003 0.001 TRP E 381 HIS 0.002 0.000 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00270 (33288) covalent geometry : angle 0.47567 (45324) hydrogen bonds : bond 0.02498 ( 1693) hydrogen bonds : angle 5.02360 ( 4611) Misc. bond : bond 0.00124 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 406 time to evaluate : 1.267 Fit side-chains REVERT: B 385 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8016 (pp) REVERT: C 385 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.7968 (pp) REVERT: D 72 TYR cc_start: 0.9231 (m-80) cc_final: 0.9000 (m-80) REVERT: D 97 ASN cc_start: 0.8701 (m110) cc_final: 0.8445 (m110) REVERT: D 107 MET cc_start: 0.8638 (mtp) cc_final: 0.8345 (ttt) REVERT: D 274 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8562 (tmtt) REVERT: D 385 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8496 (pp) REVERT: G 385 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8327 (pp) REVERT: H 355 ARG cc_start: 0.8417 (ttp-170) cc_final: 0.8132 (ptt180) REVERT: I 251 LEU cc_start: 0.8778 (tp) cc_final: 0.8535 (tp) REVERT: J 246 ASN cc_start: 0.8370 (t0) cc_final: 0.8021 (t0) REVERT: K 385 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8366 (pp) REVERT: L 86 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8685 (mtm110) outliers start: 77 outliers final: 69 residues processed: 461 average time/residue: 0.2114 time to fit residues: 159.2766 Evaluate side-chains 465 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 391 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 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 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 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 164 ASP Chi-restraints excluded: chain J residue 236 LEU 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 236 LEU Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 148 THR 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 129 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 342 optimal weight: 0.9980 chunk 264 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 191 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 109 HIS C 196 ASN D 322 GLN E 196 ASN H 196 ASN I 109 HIS L 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117546 restraints weight = 134676.886| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.90 r_work: 0.2627 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33312 Z= 0.123 Angle : 0.478 7.446 45324 Z= 0.236 Chirality : 0.044 0.144 5244 Planarity : 0.004 0.072 5904 Dihedral : 7.820 80.237 5164 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.66 % Allowed : 14.50 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.12), residues: 4260 helix: 0.70 (0.13), residues: 1704 sheet: -0.78 (0.16), residues: 792 loop : 0.20 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 355 TYR 0.024 0.001 TYR C 361 PHE 0.007 0.001 PHE J 199 TRP 0.003 0.001 TRP F 381 HIS 0.002 0.000 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00293 (33288) covalent geometry : angle 0.47849 (45324) hydrogen bonds : bond 0.02543 ( 1693) hydrogen bonds : angle 5.03007 ( 4611) Misc. bond : bond 0.00136 ( 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 477 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 398 time to evaluate : 1.270 Fit side-chains REVERT: A 72 TYR cc_start: 0.9211 (m-80) cc_final: 0.8965 (m-80) REVERT: B 385 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.7810 (pp) REVERT: C 385 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7755 (pp) REVERT: D 72 TYR cc_start: 0.9234 (m-80) cc_final: 0.8965 (m-80) REVERT: D 97 ASN cc_start: 0.8590 (m110) cc_final: 0.8314 (m110) REVERT: D 107 MET cc_start: 0.8530 (mtp) cc_final: 0.8259 (ttt) REVERT: D 274 LYS cc_start: 0.8758 (tmtt) cc_final: 0.8499 (tmtt) REVERT: D 385 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8327 (pp) REVERT: E 62 ILE cc_start: 0.8612 (mm) cc_final: 0.8341 (mt) REVERT: G 385 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8131 (pp) REVERT: H 62 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8561 (mt) REVERT: H 355 ARG cc_start: 0.8326 (ttp-170) cc_final: 0.7873 (ptt180) REVERT: I 251 LEU cc_start: 0.8656 (tp) cc_final: 0.8408 (tp) REVERT: J 246 ASN cc_start: 0.8347 (t0) cc_final: 0.7957 (t0) REVERT: K 385 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8175 (pp) REVERT: L 86 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8655 (mtm110) outliers start: 79 outliers final: 69 residues processed: 455 average time/residue: 0.1973 time to fit residues: 146.8287 Evaluate side-chains 464 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 389 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 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 89 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 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 89 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 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 164 ASP Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 GLN Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 148 THR 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 182 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 408 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 207 optimal weight: 0.0270 chunk 266 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 253 optimal weight: 0.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 109 HIS H 134 GLN H 196 ASN L 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114938 restraints weight = 130127.733| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.88 r_work: 0.2624 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 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 = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 33312 Z= 0.158 Angle : 0.503 7.701 45324 Z= 0.247 Chirality : 0.045 0.146 5244 Planarity : 0.004 0.070 5904 Dihedral : 7.894 80.326 5162 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.66 % Allowed : 14.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.12), residues: 4260 helix: 0.55 (0.12), residues: 1716 sheet: -0.99 (0.15), residues: 816 loop : 0.21 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 355 TYR 0.031 0.001 TYR D 361 PHE 0.008 0.001 PHE D 199 TRP 0.004 0.001 TRP E 381 HIS 0.003 0.000 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00384 (33288) covalent geometry : angle 0.50348 (45324) hydrogen bonds : bond 0.02741 ( 1693) hydrogen bonds : angle 5.15615 ( 4611) Misc. bond : bond 0.00175 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 389 time to evaluate : 1.280 Fit side-chains REVERT: B 385 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.7870 (pp) REVERT: C 62 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8504 (mt) REVERT: C 385 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7741 (pp) REVERT: D 72 TYR cc_start: 0.9274 (m-80) cc_final: 0.9006 (m-80) REVERT: D 97 ASN cc_start: 0.8616 (m110) cc_final: 0.8345 (m110) REVERT: D 107 MET cc_start: 0.8519 (mtp) cc_final: 0.8274 (ttt) REVERT: D 274 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8537 (tmtt) REVERT: D 385 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8305 (pp) REVERT: G 385 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8161 (pp) REVERT: H 62 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8508 (mt) REVERT: I 251 LEU cc_start: 0.8704 (tp) cc_final: 0.8448 (tp) REVERT: J 246 ASN cc_start: 0.8392 (t0) cc_final: 0.8006 (t0) REVERT: K 246 ASN cc_start: 0.8148 (t0) cc_final: 0.7850 (t0) REVERT: K 385 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8227 (pp) REVERT: L 35 LYS cc_start: 0.7760 (pttm) cc_final: 0.7516 (pttm) REVERT: L 86 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8648 (mtm110) outliers start: 79 outliers final: 69 residues processed: 446 average time/residue: 0.1967 time to fit residues: 142.8697 Evaluate side-chains 459 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 383 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 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 62 ILE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 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 89 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 385 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 164 ASP Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 237 GLN Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 237 GLN Chi-restraints excluded: chain K residue 350 GLU Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 148 THR 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 210 optimal weight: 5.9990 chunk 147 optimal weight: 0.0670 chunk 336 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 292 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN B 85 ASN B 109 HIS E 196 ASN L 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118394 restraints weight = 135063.117| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.05 r_work: 0.2976 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1964 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= 0.100 Angle : 0.469 7.344 45324 Z= 0.232 Chirality : 0.044 0.145 5244 Planarity : 0.004 0.067 5904 Dihedral : 7.729 78.511 5162 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.54 % Allowed : 14.56 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.12), residues: 4260 helix: 0.88 (0.13), residues: 1704 sheet: -0.72 (0.16), residues: 792 loop : 0.25 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 355 TYR 0.027 0.001 TYR C 361 PHE 0.007 0.001 PHE L 121 TRP 0.001 0.000 TRP D 381 HIS 0.002 0.000 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00230 (33288) covalent geometry : angle 0.46886 (45324) hydrogen bonds : bond 0.02437 ( 1693) hydrogen bonds : angle 4.94498 ( 4611) Misc. bond : bond 0.00103 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6967.96 seconds wall clock time: 120 minutes 18.86 seconds (7218.86 seconds total)