Starting phenix.real_space_refine on Fri Sep 11 11:23:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cp5_7547/09_2026/6cp5_7547.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cp5_7547/09_2026/6cp5_7547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6cp5_7547/09_2026/6cp5_7547.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cp5_7547/09_2026/6cp5_7547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cp5_7547/09_2026/6cp5_7547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cp5_7547/09_2026/6cp5_7547.map" model { file = "/net/cci-nas-00/data/ceres_data/6cp5_7547/09_2026/6cp5_7547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cp5_7547/09_2026/6cp5_7547.cif" } resolution = 4.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 6335 2.51 5 N 1422 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9413 Number of models: 1 Model: "" Number of chains: 19 Chain: "K" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 364 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "X" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1772 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "Z" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 386 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 52} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "7" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 520 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 63} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 522 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 63} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "N" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 112 Unusual residues: {'EFO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'EFO': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'EFO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.13, per 1000 atoms: 0.23 Number of scatterers: 9413 At special positions: 0 Unit cell: (84.87, 115.62, 114.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1605 8.00 N 1422 7.00 C 6335 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=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 285.6 milliseconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'K' and resid 2 through 15 removed outlier: 3.865A pdb=" N ALA K 6 " --> pdb=" O GLN K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 38 removed outlier: 4.384A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 43 through 74 Proline residue: K 49 - end of helix removed outlier: 3.591A pdb=" N LEU K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS K 65 " --> pdb=" O THR K 61 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU K 66 " --> pdb=" O GLY K 62 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 17 removed outlier: 4.082A pdb=" N ILE L 17 " --> pdb=" O GLY L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 39 removed outlier: 4.429A pdb=" N ALA L 27 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG L 39 " --> pdb=" O ASN L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 42 No H-bonds generated for 'chain 'L' and resid 40 through 42' Processing helix chain 'L' and resid 43 through 74 Proline residue: L 49 - end of helix removed outlier: 3.647A pdb=" N LEU L 57 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS L 65 " --> pdb=" O THR L 61 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 15 Processing helix chain 'M' and resid 16 through 18 No H-bonds generated for 'chain 'M' and resid 16 through 18' Processing helix chain 'M' and resid 19 through 40 removed outlier: 3.798A pdb=" N ALA M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 74 Proline residue: M 49 - end of helix removed outlier: 3.764A pdb=" N LEU M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU M 66 " --> pdb=" O GLY M 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE M 74 " --> pdb=" O PHE M 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 16 through 18 No H-bonds generated for 'chain 'N' and resid 16 through 18' Processing helix chain 'N' and resid 19 through 38 removed outlier: 5.118A pdb=" N ALA N 27 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE N 28 " --> pdb=" O ILE N 24 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 74 Proline residue: N 49 - end of helix removed outlier: 4.745A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 15 through 18 removed outlier: 4.429A pdb=" N GLY O 18 " --> pdb=" O SER O 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 15 through 18' Processing helix chain 'O' and resid 19 through 38 removed outlier: 4.759A pdb=" N ALA O 27 " --> pdb=" O GLY O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 74 Proline residue: O 49 - end of helix removed outlier: 3.702A pdb=" N LEU O 57 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY O 62 " --> pdb=" O SER O 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.689A pdb=" N ALA P 6 " --> pdb=" O GLN P 2 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE P 14 " --> pdb=" O ILE P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 17 No H-bonds generated for 'chain 'P' and resid 15 through 17' Processing helix chain 'P' and resid 18 through 38 removed outlier: 4.071A pdb=" N ALA P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 59 removed outlier: 4.103A pdb=" N MET P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 74 removed outlier: 4.234A pdb=" N VAL P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER P 69 " --> pdb=" O CYS P 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 15 removed outlier: 4.044A pdb=" N ALA Q 6 " --> pdb=" O GLN Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 18 No H-bonds generated for 'chain 'Q' and resid 16 through 18' Processing helix chain 'Q' and resid 19 through 39 removed outlier: 4.953A pdb=" N ALA Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL Q 37 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG Q 39 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 74 removed outlier: 4.046A pdb=" N MET Q 50 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS Q 65 " --> pdb=" O THR Q 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Q 66 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL Q 68 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.643A pdb=" N ALA R 7 " --> pdb=" O LEU R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 18 No H-bonds generated for 'chain 'R' and resid 16 through 18' Processing helix chain 'R' and resid 19 through 40 removed outlier: 3.840A pdb=" N ALA R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 72 Proline residue: R 49 - end of helix removed outlier: 3.781A pdb=" N LEU R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N THR R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY R 62 " --> pdb=" O SER R 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 15 Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 19 through 39 removed outlier: 4.274A pdb=" N ALA S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE S 28 " --> pdb=" O ILE S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 42 No H-bonds generated for 'chain 'S' and resid 40 through 42' Processing helix chain 'S' and resid 43 through 74 Proline residue: S 49 - end of helix removed outlier: 3.558A pdb=" N GLY S 54 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS S 65 " --> pdb=" O THR S 61 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 16 through 18 No H-bonds generated for 'chain 'T' and resid 16 through 18' Processing helix chain 'T' and resid 19 through 38 removed outlier: 4.464A pdb=" N ILE T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 42 No H-bonds generated for 'chain 'T' and resid 40 through 42' Processing helix chain 'T' and resid 43 through 62 Proline residue: T 49 - end of helix removed outlier: 3.552A pdb=" N LEU T 53 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR T 61 " --> pdb=" O LEU T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 74 Processing helix chain '8' and resid 8 through 48 removed outlier: 5.437A pdb=" N LEU 8 32 " --> pdb=" O SER 8 28 " (cutoff:3.500A) Proline residue: 8 33 - end of helix removed outlier: 3.736A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 27 through 45 removed outlier: 3.726A pdb=" N TYR X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 78 removed outlier: 3.743A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE X 77 " --> pdb=" O THR X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 84 No H-bonds generated for 'chain 'X' and resid 82 through 84' Processing helix chain 'X' and resid 85 through 103 removed outlier: 3.783A pdb=" N PHE X 93 " --> pdb=" O ILE X 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU X 101 " --> pdb=" O PHE X 97 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER X 103 " --> pdb=" O ALA X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 138 Processing helix chain 'X' and resid 139 through 146 removed outlier: 3.551A pdb=" N PHE X 142 " --> pdb=" O TRP X 139 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU X 144 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 153 No H-bonds generated for 'chain 'X' and resid 151 through 153' Processing helix chain 'X' and resid 154 through 198 removed outlier: 3.799A pdb=" N VAL X 159 " --> pdb=" O VAL X 155 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU X 162 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE X 167 " --> pdb=" O THR X 163 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA X 170 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA X 192 " --> pdb=" O MET X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 207 removed outlier: 3.596A pdb=" N VAL X 207 " --> pdb=" O PHE X 204 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 247 removed outlier: 4.223A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 106 removed outlier: 4.820A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.563A pdb=" N ARG Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) Processing helix chain '7' and resid 108 through 125 removed outlier: 3.766A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 142 Processing helix chain '7' and resid 142 through 156 removed outlier: 4.440A pdb=" N ASP 7 146 " --> pdb=" O LYS 7 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 31 removed outlier: 4.047A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 56 Processing helix chain 'U' and resid 63 through 85 removed outlier: 3.586A pdb=" N TRP U 67 " --> pdb=" O GLY U 63 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 34 708 hydrogen bonds defined for protein. 2112 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: 1.45 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1447 1.33 - 1.45: 2458 1.45 - 1.57: 5602 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 9599 Sorted by residual: bond pdb=" C19 EFO N 101 " pdb=" C20 EFO N 101 " ideal model delta sigma weight residual 1.453 1.390 0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" C19 EFO N 102 " pdb=" C20 EFO N 102 " ideal model delta sigma weight residual 1.453 1.390 0.063 2.00e-02 2.50e+03 9.79e+00 bond pdb=" C19 EFO O 101 " pdb=" C20 EFO O 101 " ideal model delta sigma weight residual 1.453 1.391 0.062 2.00e-02 2.50e+03 9.62e+00 bond pdb=" C19 EFO P 101 " pdb=" C20 EFO P 101 " ideal model delta sigma weight residual 1.453 1.391 0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" SD FME P 1 " pdb=" CE FME P 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 7.15e+00 ... (remaining 9594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 12473 1.99 - 3.98: 423 3.98 - 5.97: 107 5.97 - 7.97: 20 7.97 - 9.96: 6 Bond angle restraints: 13029 Sorted by residual: angle pdb=" C GLY U 37 " pdb=" N PRO U 38 " pdb=" CA PRO U 38 " ideal model delta sigma weight residual 119.84 129.80 -9.96 1.25e+00 6.40e-01 6.35e+01 angle pdb=" N GLU O 59 " pdb=" CA GLU O 59 " pdb=" C GLU O 59 " ideal model delta sigma weight residual 112.23 104.26 7.97 1.26e+00 6.30e-01 4.00e+01 angle pdb=" N LEU P 71 " pdb=" CA LEU P 71 " pdb=" C LEU P 71 " ideal model delta sigma weight residual 111.28 105.06 6.22 1.09e+00 8.42e-01 3.26e+01 angle pdb=" N PRO P 49 " pdb=" CA PRO P 49 " pdb=" C PRO P 49 " ideal model delta sigma weight residual 113.47 105.58 7.89 1.43e+00 4.89e-01 3.04e+01 angle pdb=" C GLU P 59 " pdb=" N ALA P 60 " pdb=" CA ALA P 60 " ideal model delta sigma weight residual 126.45 118.33 8.12 1.77e+00 3.19e-01 2.10e+01 ... (remaining 13024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 5606 33.37 - 66.74: 115 66.74 - 100.11: 26 100.11 - 133.49: 40 133.49 - 166.86: 49 Dihedral angle restraints: 5836 sinusoidal: 2357 harmonic: 3479 Sorted by residual: dihedral pdb=" CA PHE 8 30 " pdb=" C PHE 8 30 " pdb=" N PHE 8 31 " pdb=" CA PHE 8 31 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" C26 EFO N 102 " pdb=" C27 EFO N 102 " pdb=" C28 EFO N 102 " pdb=" C29 EFO N 102 " ideal model delta sinusoidal sigma weight residual -86.80 80.06 -166.86 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C26 EFO N 101 " pdb=" C27 EFO N 101 " pdb=" C28 EFO N 101 " pdb=" C29 EFO N 101 " ideal model delta sinusoidal sigma weight residual -86.80 79.98 -166.78 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 5833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1482 0.073 - 0.147: 123 0.147 - 0.220: 13 0.220 - 0.293: 8 0.293 - 0.367: 12 Chirality restraints: 1638 Sorted by residual: chirality pdb=" C29 EFO N 101 " pdb=" C28 EFO N 101 " pdb=" C2D EFO N 101 " pdb=" C30 EFO N 101 " both_signs ideal model delta sigma weight residual False -2.28 -2.65 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C27 EFO P 101 " pdb=" C26 EFO P 101 " pdb=" C28 EFO P 101 " pdb=" C2C EFO P 101 " both_signs ideal model delta sigma weight residual False 2.26 2.63 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C29 EFO P 101 " pdb=" C28 EFO P 101 " pdb=" C2D EFO P 101 " pdb=" C30 EFO P 101 " both_signs ideal model delta sigma weight residual False -2.28 -2.64 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1635 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 EFO O 101 " 0.162 2.00e-02 2.50e+03 2.48e-01 6.16e+02 pdb=" C20 EFO O 101 " -0.383 2.00e-02 2.50e+03 pdb=" C21 EFO O 101 " 0.268 2.00e-02 2.50e+03 pdb=" C22 EFO O 101 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 EFO O 101 " -0.197 2.00e-02 2.50e+03 2.46e-01 6.05e+02 pdb=" C18 EFO O 101 " 0.138 2.00e-02 2.50e+03 pdb=" C19 EFO O 101 " 0.332 2.00e-02 2.50e+03 pdb=" C20 EFO O 101 " -0.272 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C33 EFO P 101 " 0.246 2.00e-02 2.50e+03 2.33e-01 5.44e+02 pdb=" C34 EFO P 101 " -0.330 2.00e-02 2.50e+03 pdb=" C35 EFO P 101 " -0.108 2.00e-02 2.50e+03 pdb=" C36 EFO P 101 " 0.192 2.00e-02 2.50e+03 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 38 2.41 - 3.03: 6331 3.03 - 3.65: 15233 3.65 - 4.28: 21717 4.28 - 4.90: 34172 Nonbonded interactions: 77491 Sorted by model distance: nonbonded pdb=" O LEU Q 63 " pdb=" N CYS Q 65 " model vdw 1.785 3.120 nonbonded pdb=" O SER Q 58 " pdb=" OG1 THR Q 61 " model vdw 1.809 3.040 nonbonded pdb=" O ILE X 160 " pdb=" OG1 THR X 163 " model vdw 1.901 3.040 nonbonded pdb=" CD1 LEU O 57 " pdb=" CZ PHE P 55 " model vdw 1.948 3.760 nonbonded pdb=" CD1 LEU O 57 " pdb=" CE2 PHE P 55 " model vdw 2.004 3.760 ... (remaining 77486 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'L' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'M' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'N' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 65 or (resid 66 and (name N or name C \ A or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'Q' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 74)) selection = (chain 'R' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'S' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'T' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.810 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.004 0.063 9599 Z= 0.224 Angle : 0.907 9.958 13029 Z= 0.480 Chirality : 0.056 0.367 1638 Planarity : 0.015 0.248 1561 Dihedral : 25.760 166.857 3610 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.21 % Favored : 92.03 % Rotamer: Outliers : 2.24 % Allowed : 8.64 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -4.36 (0.20), residues: 1192 helix: -2.56 (0.13), residues: 973 sheet: None (None), residues: 0 loop : -3.21 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 57 TYR 0.014 0.001 TYR J 25 PHE 0.020 0.001 PHE O 70 TRP 0.011 0.001 TRP U 67 HIS 0.003 0.001 HIS U 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.22 ( 9599) covalent geometry : angle 0.90677 / 0.48 (13029) hydrogen bonds : bond 0.18812 / 12.36 ( 708) hydrogen bonds : angle 7.67507 / 5.30 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 613 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 43 ILE cc_start: 0.8845 (tp) cc_final: 0.8622 (tp) REVERT: K 67 MET cc_start: 0.8852 (ttp) cc_final: 0.8574 (ttm) REVERT: L 5 LEU cc_start: 0.7455 (pt) cc_final: 0.6754 (mp) REVERT: L 39 ARG cc_start: 0.7325 (ptm-80) cc_final: 0.7000 (tpt170) REVERT: L 47 VAL cc_start: 0.9000 (t) cc_final: 0.8774 (p) REVERT: L 67 MET cc_start: 0.7773 (pp-130) cc_final: 0.7318 (tpt) REVERT: L 68 VAL cc_start: 0.7931 (t) cc_final: 0.7693 (t) REVERT: M 44 LYS cc_start: 0.8549 (ttmt) cc_final: 0.7908 (tptp) REVERT: M 52 ILE cc_start: 0.8648 (tt) cc_final: 0.8436 (tt) REVERT: M 67 MET cc_start: 0.8672 (pp-130) cc_final: 0.8308 (ppp) REVERT: P 5 LEU cc_start: 0.8229 (pt) cc_final: 0.7616 (tp) REVERT: Q 26 ILE cc_start: 0.8297 (pt) cc_final: 0.7880 (pt) REVERT: Q 38 SER cc_start: 0.8387 (p) cc_final: 0.7922 (m) REVERT: R 3 LEU cc_start: 0.6898 (tm) cc_final: 0.6046 (mt) REVERT: R 5 LEU cc_start: 0.8290 (pt) cc_final: 0.7107 (pt) REVERT: R 26 ILE cc_start: 0.8505 (pt) cc_final: 0.7836 (mt) REVERT: S 43 ILE cc_start: 0.8345 (tt) cc_final: 0.8130 (tp) REVERT: 8 26 LEU cc_start: 0.8733 (tt) cc_final: 0.8309 (tt) REVERT: X 31 LEU cc_start: 0.8573 (tt) cc_final: 0.8184 (pp) REVERT: X 56 SER cc_start: 0.7112 (m) cc_final: 0.6825 (m) REVERT: X 81 ASN cc_start: 0.8410 (p0) cc_final: 0.8186 (p0) REVERT: X 84 LEU cc_start: 0.8476 (mp) cc_final: 0.8150 (tp) REVERT: X 92 LEU cc_start: 0.8662 (mt) cc_final: 0.8038 (mt) REVERT: X 98 ILE cc_start: 0.8619 (mm) cc_final: 0.8394 (mm) REVERT: X 120 SER cc_start: 0.8716 (t) cc_final: 0.8507 (p) REVERT: X 164 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6456 (pp) REVERT: X 190 ILE cc_start: 0.7885 (mt) cc_final: 0.7524 (mm) REVERT: 7 128 ARG cc_start: 0.6699 (ttm170) cc_final: 0.6437 (ttm-80) REVERT: 7 148 LYS cc_start: 0.7935 (tttp) cc_final: 0.6727 (ttmt) REVERT: U 32 LYS cc_start: 0.5617 (ttmt) cc_final: 0.5354 (ttpt) REVERT: U 68 HIS cc_start: 0.7759 (m-70) cc_final: 0.7342 (t-170) REVERT: J 1 MET cc_start: 0.6384 (ttp) cc_final: 0.5496 (mtt) outliers start: 21 outliers final: 12 residues processed: 625 average time/residue: 0.0844 time to fit residues: 75.3685 Evaluate side-chains 450 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 437 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 2 GLN X 71 ASN X 185 HIS ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.124129 restraints weight = 23559.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126305 restraints weight = 15771.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127922 restraints weight = 11756.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.128864 restraints weight = 9504.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129753 restraints weight = 8246.515| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9599 Z= 0.194 Angle : 0.897 12.547 13029 Z= 0.405 Chirality : 0.047 0.330 1638 Planarity : 0.005 0.053 1561 Dihedral : 30.353 178.823 1704 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.61 % Favored : 95.22 % Rotamer: Outliers : 0.43 % Allowed : 5.76 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.34 (0.23), residues: 1192 helix: -1.14 (0.15), residues: 995 sheet: None (None), residues: 0 loop : -2.74 (0.47), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 8 37 TYR 0.020 0.002 TYR R 9 PHE 0.050 0.002 PHE O 64 TRP 0.017 0.002 TRP X 126 HIS 0.006 0.002 HIS U 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 9599) covalent geometry : angle 0.89660 / 0.41 (13029) hydrogen bonds : bond 0.04750 / 3.17 ( 708) hydrogen bonds : angle 4.98802 / 3.48 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 508 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.8035 (tt) cc_final: 0.7380 (mt) REVERT: K 63 LEU cc_start: 0.7938 (mt) cc_final: 0.7639 (mt) REVERT: L 3 LEU cc_start: 0.8764 (tt) cc_final: 0.8467 (mp) REVERT: L 5 LEU cc_start: 0.7401 (pt) cc_final: 0.6999 (mp) REVERT: L 39 ARG cc_start: 0.7613 (ptm-80) cc_final: 0.6836 (tmt-80) REVERT: L 57 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8172 (pt) REVERT: P 2 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7590 (tp40) REVERT: P 5 LEU cc_start: 0.8369 (pt) cc_final: 0.7404 (pt) REVERT: P 48 PHE cc_start: 0.8558 (t80) cc_final: 0.8355 (t80) REVERT: Q 30 PHE cc_start: 0.8210 (m-80) cc_final: 0.7921 (m-80) REVERT: Q 48 PHE cc_start: 0.8047 (t80) cc_final: 0.7823 (t80) REVERT: Q 50 MET cc_start: 0.8665 (ptp) cc_final: 0.8338 (ptm) REVERT: R 3 LEU cc_start: 0.6977 (tt) cc_final: 0.6251 (mt) REVERT: R 5 LEU cc_start: 0.8284 (pt) cc_final: 0.7096 (pt) REVERT: R 26 ILE cc_start: 0.8503 (pt) cc_final: 0.7782 (mt) REVERT: R 64 PHE cc_start: 0.8012 (m-10) cc_final: 0.7646 (m-10) REVERT: S 43 ILE cc_start: 0.8337 (tt) cc_final: 0.7866 (mm) REVERT: 8 34 MET cc_start: 0.8188 (ppp) cc_final: 0.7972 (ppp) REVERT: 8 37 ARG cc_start: 0.8267 (ptm160) cc_final: 0.7737 (ptm160) REVERT: X 31 LEU cc_start: 0.8728 (tt) cc_final: 0.8146 (pp) REVERT: X 72 MET cc_start: 0.8894 (tmm) cc_final: 0.8509 (tmm) REVERT: X 81 ASN cc_start: 0.8396 (p0) cc_final: 0.8150 (p0) REVERT: X 84 LEU cc_start: 0.8686 (mp) cc_final: 0.8119 (tp) REVERT: X 92 LEU cc_start: 0.8465 (mt) cc_final: 0.8156 (mt) REVERT: X 104 MET cc_start: 0.7778 (tpt) cc_final: 0.7474 (tpt) REVERT: X 224 PHE cc_start: 0.7493 (t80) cc_final: 0.7276 (t80) REVERT: X 236 ILE cc_start: 0.9011 (mm) cc_final: 0.8607 (tp) REVERT: X 241 TYR cc_start: 0.8148 (m-10) cc_final: 0.7945 (m-80) REVERT: Z 93 ASN cc_start: 0.7961 (t0) cc_final: 0.7734 (m-40) REVERT: 7 128 ARG cc_start: 0.6851 (ttm170) cc_final: 0.6492 (ttm-80) REVERT: 7 130 PHE cc_start: 0.7113 (p90) cc_final: 0.6485 (p90) REVERT: 7 169 ASN cc_start: 0.6622 (p0) cc_final: 0.6291 (p0) REVERT: 7 173 MET cc_start: 0.5271 (pmm) cc_final: 0.4699 (pmm) REVERT: U 50 ARG cc_start: 0.8097 (mpt-90) cc_final: 0.7846 (mpp80) REVERT: J 2 LEU cc_start: 0.7495 (mt) cc_final: 0.7158 (mt) outliers start: 4 outliers final: 0 residues processed: 511 average time/residue: 0.0838 time to fit residues: 61.9378 Evaluate side-chains 411 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 40 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.143220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.124200 restraints weight = 23875.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126904 restraints weight = 15658.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.128582 restraints weight = 11390.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129767 restraints weight = 9184.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.130291 restraints weight = 7879.791| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9599 Z= 0.151 Angle : 0.849 11.243 13029 Z= 0.381 Chirality : 0.046 0.375 1638 Planarity : 0.004 0.050 1561 Dihedral : 27.777 177.572 1704 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.69 % Favored : 96.14 % Rotamer: Outliers : 0.53 % Allowed : 6.40 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.36 (0.23), residues: 1192 helix: -0.44 (0.16), residues: 998 sheet: None (None), residues: 0 loop : -2.62 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 8 42 TYR 0.026 0.002 TYR P 9 PHE 0.043 0.002 PHE T 70 TRP 0.037 0.002 TRP X 126 HIS 0.005 0.001 HIS U 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 9599) covalent geometry : angle 0.84879 / 0.38 (13029) hydrogen bonds : bond 0.04295 / 2.85 ( 708) hydrogen bonds : angle 4.52284 / 3.15 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 500 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7986 (tt) cc_final: 0.7267 (mt) REVERT: L 3 LEU cc_start: 0.8753 (tt) cc_final: 0.8393 (mt) REVERT: L 5 LEU cc_start: 0.7502 (pt) cc_final: 0.7071 (mp) REVERT: L 39 ARG cc_start: 0.7671 (ptm-80) cc_final: 0.6883 (tmt-80) REVERT: L 40 ASN cc_start: 0.7811 (t0) cc_final: 0.7489 (t0) REVERT: L 63 LEU cc_start: 0.8822 (mt) cc_final: 0.8542 (mt) REVERT: M 43 ILE cc_start: 0.8864 (tp) cc_final: 0.8591 (tt) REVERT: M 67 MET cc_start: 0.8140 (tmm) cc_final: 0.7926 (tmm) REVERT: N 2 GLN cc_start: 0.5264 (pm20) cc_final: 0.5035 (pm20) REVERT: N 73 LEU cc_start: 0.8842 (tp) cc_final: 0.8363 (tp) REVERT: P 5 LEU cc_start: 0.8129 (pt) cc_final: 0.7886 (pt) REVERT: Q 2 GLN cc_start: 0.7579 (mp10) cc_final: 0.7375 (mp10) REVERT: Q 5 LEU cc_start: 0.8254 (pt) cc_final: 0.7224 (mp) REVERT: Q 48 PHE cc_start: 0.7993 (t80) cc_final: 0.7788 (t80) REVERT: Q 50 MET cc_start: 0.8506 (ptp) cc_final: 0.7864 (ptt) REVERT: Q 67 MET cc_start: 0.7513 (ptm) cc_final: 0.7200 (tmm) REVERT: R 3 LEU cc_start: 0.6962 (tt) cc_final: 0.6150 (mt) REVERT: R 5 LEU cc_start: 0.8211 (pt) cc_final: 0.7395 (pt) REVERT: S 46 THR cc_start: 0.8736 (m) cc_final: 0.8044 (p) REVERT: S 47 VAL cc_start: 0.9080 (t) cc_final: 0.8863 (t) REVERT: T 4 VAL cc_start: 0.7730 (t) cc_final: 0.7454 (t) REVERT: 8 10 MET cc_start: 0.7081 (mmp) cc_final: 0.5898 (mpp) REVERT: 8 31 PHE cc_start: 0.7877 (m-80) cc_final: 0.7639 (m-80) REVERT: 8 34 MET cc_start: 0.8116 (ppp) cc_final: 0.7598 (ppp) REVERT: 8 35 ILE cc_start: 0.9384 (mt) cc_final: 0.9139 (mm) REVERT: 8 37 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7574 (ptm160) REVERT: X 31 LEU cc_start: 0.8570 (tt) cc_final: 0.8059 (pp) REVERT: X 67 ASP cc_start: 0.7599 (t70) cc_final: 0.7358 (t70) REVERT: X 72 MET cc_start: 0.8947 (tmm) cc_final: 0.8509 (tmm) REVERT: X 84 LEU cc_start: 0.8575 (mp) cc_final: 0.8108 (tp) REVERT: X 92 LEU cc_start: 0.8492 (mt) cc_final: 0.7968 (mt) REVERT: X 98 ILE cc_start: 0.9034 (mm) cc_final: 0.8740 (mm) REVERT: X 236 ILE cc_start: 0.8999 (mm) cc_final: 0.8633 (tp) REVERT: Z 66 THR cc_start: 0.7633 (p) cc_final: 0.7372 (p) REVERT: 7 128 ARG cc_start: 0.6967 (ttm170) cc_final: 0.6699 (ttm-80) REVERT: 7 130 PHE cc_start: 0.7207 (p90) cc_final: 0.6542 (p90) REVERT: 7 136 ASP cc_start: 0.7811 (m-30) cc_final: 0.7528 (m-30) REVERT: 7 173 MET cc_start: 0.5220 (pmm) cc_final: 0.4824 (pmm) REVERT: U 81 GLU cc_start: 0.6307 (pp20) cc_final: 0.5903 (mt-10) REVERT: J 27 MET cc_start: 0.7658 (tpp) cc_final: 0.7224 (tmm) outliers start: 5 outliers final: 0 residues processed: 503 average time/residue: 0.0825 time to fit residues: 60.7437 Evaluate side-chains 429 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 4 optimal weight: 0.0970 chunk 70 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 ASN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN U 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.142751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125106 restraints weight = 23973.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127325 restraints weight = 15771.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.129030 restraints weight = 11895.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.130092 restraints weight = 9439.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.131009 restraints weight = 8097.386| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9599 Z= 0.159 Angle : 0.856 11.202 13029 Z= 0.385 Chirality : 0.045 0.377 1638 Planarity : 0.004 0.063 1561 Dihedral : 25.898 177.242 1704 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.53 % Favored : 95.30 % Rotamer: Outliers : 0.32 % Allowed : 4.48 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.89 (0.24), residues: 1192 helix: -0.13 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -2.41 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 50 TYR 0.023 0.002 TYR X 241 PHE 0.034 0.002 PHE 8 17 TRP 0.048 0.003 TRP X 126 HIS 0.003 0.001 HIS U 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9599) covalent geometry : angle 0.85623 / 0.38 (13029) hydrogen bonds : bond 0.04049 / 2.70 ( 708) hydrogen bonds : angle 4.44986 / 3.09 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 492 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7937 (tt) cc_final: 0.7209 (mt) REVERT: L 3 LEU cc_start: 0.8640 (tt) cc_final: 0.8302 (mt) REVERT: L 5 LEU cc_start: 0.7456 (pt) cc_final: 0.6969 (mp) REVERT: L 39 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.6919 (tmt-80) REVERT: L 40 ASN cc_start: 0.7840 (t0) cc_final: 0.7436 (t0) REVERT: M 43 ILE cc_start: 0.8946 (tp) cc_final: 0.8598 (tt) REVERT: M 63 LEU cc_start: 0.9104 (mm) cc_final: 0.8630 (mt) REVERT: P 5 LEU cc_start: 0.8148 (pt) cc_final: 0.7468 (pt) REVERT: Q 5 LEU cc_start: 0.8385 (pt) cc_final: 0.7281 (mp) REVERT: Q 48 PHE cc_start: 0.7996 (t80) cc_final: 0.7767 (t80) REVERT: Q 50 MET cc_start: 0.8620 (ptp) cc_final: 0.7940 (ptt) REVERT: Q 64 PHE cc_start: 0.7032 (m-80) cc_final: 0.6600 (m-80) REVERT: Q 67 MET cc_start: 0.7376 (ptm) cc_final: 0.7157 (tmm) REVERT: R 3 LEU cc_start: 0.6849 (tt) cc_final: 0.6271 (mt) REVERT: R 5 LEU cc_start: 0.8267 (pt) cc_final: 0.7114 (pt) REVERT: S 34 ILE cc_start: 0.9433 (mt) cc_final: 0.9180 (tp) REVERT: 8 25 ILE cc_start: 0.8941 (mt) cc_final: 0.8630 (mt) REVERT: 8 29 GLN cc_start: 0.8385 (mp10) cc_final: 0.7861 (mp10) REVERT: 8 34 MET cc_start: 0.8207 (ppp) cc_final: 0.7707 (ppp) REVERT: 8 35 ILE cc_start: 0.9438 (mt) cc_final: 0.9191 (mm) REVERT: 8 37 ARG cc_start: 0.8071 (ptm160) cc_final: 0.7613 (ptm160) REVERT: X 31 LEU cc_start: 0.8566 (tt) cc_final: 0.7991 (pp) REVERT: X 54 ILE cc_start: 0.8572 (mm) cc_final: 0.8284 (mm) REVERT: X 67 ASP cc_start: 0.7455 (t70) cc_final: 0.7196 (t70) REVERT: X 72 MET cc_start: 0.9126 (tmm) cc_final: 0.8585 (tmm) REVERT: X 81 ASN cc_start: 0.8376 (p0) cc_final: 0.8052 (p0) REVERT: X 84 LEU cc_start: 0.8660 (mp) cc_final: 0.8037 (tp) REVERT: X 98 ILE cc_start: 0.9001 (mm) cc_final: 0.8765 (mm) REVERT: X 236 ILE cc_start: 0.9053 (mm) cc_final: 0.8717 (tp) REVERT: Z 85 MET cc_start: 0.8306 (mmt) cc_final: 0.7945 (mmt) REVERT: 7 128 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6505 (ttm-80) REVERT: 7 131 ASP cc_start: 0.8784 (t0) cc_final: 0.8530 (t0) REVERT: 7 136 ASP cc_start: 0.7969 (m-30) cc_final: 0.7751 (m-30) REVERT: 7 173 MET cc_start: 0.5187 (pmm) cc_final: 0.4937 (pmm) REVERT: U 81 GLU cc_start: 0.6212 (pp20) cc_final: 0.5867 (mt-10) outliers start: 3 outliers final: 0 residues processed: 493 average time/residue: 0.0844 time to fit residues: 60.6022 Evaluate side-chains 418 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 ASN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.142369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124799 restraints weight = 23703.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127254 restraints weight = 15417.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.128930 restraints weight = 11232.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130102 restraints weight = 8917.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.130811 restraints weight = 7569.489| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9599 Z= 0.157 Angle : 0.863 12.145 13029 Z= 0.384 Chirality : 0.045 0.385 1638 Planarity : 0.004 0.052 1561 Dihedral : 24.189 177.938 1704 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.86 % Favored : 95.97 % Rotamer: Outliers : 0.11 % Allowed : 5.01 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.74 (0.24), residues: 1192 helix: -0.01 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -2.45 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 50 TYR 0.023 0.002 TYR R 9 PHE 0.027 0.002 PHE 8 31 TRP 0.061 0.003 TRP X 126 HIS 0.004 0.001 HIS U 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9599) covalent geometry : angle 0.86350 / 0.38 (13029) hydrogen bonds : bond 0.03972 / 2.65 ( 708) hydrogen bonds : angle 4.36699 / 3.03 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 493 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7944 (tt) cc_final: 0.7156 (mt) REVERT: L 3 LEU cc_start: 0.8612 (tt) cc_final: 0.8221 (mt) REVERT: L 5 LEU cc_start: 0.7427 (pt) cc_final: 0.6939 (mp) REVERT: L 39 ARG cc_start: 0.7825 (ptm-80) cc_final: 0.6917 (tmt-80) REVERT: L 40 ASN cc_start: 0.7855 (t0) cc_final: 0.7404 (t0) REVERT: L 63 LEU cc_start: 0.8745 (mt) cc_final: 0.8536 (mt) REVERT: M 63 LEU cc_start: 0.9064 (mm) cc_final: 0.8499 (mt) REVERT: P 2 GLN cc_start: 0.7759 (tp40) cc_final: 0.7359 (tp40) REVERT: P 5 LEU cc_start: 0.8095 (pt) cc_final: 0.7881 (pt) REVERT: P 19 LEU cc_start: 0.7745 (pp) cc_final: 0.7314 (pp) REVERT: Q 5 LEU cc_start: 0.8356 (pt) cc_final: 0.7317 (mp) REVERT: Q 50 MET cc_start: 0.8404 (ptp) cc_final: 0.7905 (ptt) REVERT: Q 67 MET cc_start: 0.7280 (ptm) cc_final: 0.6957 (tmm) REVERT: Q 72 LEU cc_start: 0.7440 (tp) cc_final: 0.7201 (tp) REVERT: R 2 GLN cc_start: 0.6421 (pm20) cc_final: 0.6200 (pm20) REVERT: R 3 LEU cc_start: 0.7015 (tt) cc_final: 0.6185 (mt) REVERT: R 5 LEU cc_start: 0.8236 (pt) cc_final: 0.7106 (pt) REVERT: R 59 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7770 (tt0) REVERT: S 34 ILE cc_start: 0.9486 (mt) cc_final: 0.9182 (tp) REVERT: 8 29 GLN cc_start: 0.8262 (mp10) cc_final: 0.7966 (mp10) REVERT: 8 34 MET cc_start: 0.8233 (ppp) cc_final: 0.7821 (ppp) REVERT: 8 35 ILE cc_start: 0.9425 (mt) cc_final: 0.9151 (mm) REVERT: 8 37 ARG cc_start: 0.7878 (ptm160) cc_final: 0.6841 (ptm160) REVERT: X 31 LEU cc_start: 0.8551 (tt) cc_final: 0.8006 (pp) REVERT: X 67 ASP cc_start: 0.7452 (t70) cc_final: 0.7217 (t70) REVERT: X 72 MET cc_start: 0.9197 (tmm) cc_final: 0.8627 (tmm) REVERT: X 84 LEU cc_start: 0.8635 (mp) cc_final: 0.7934 (tp) REVERT: X 98 ILE cc_start: 0.8999 (mm) cc_final: 0.8740 (mm) REVERT: X 236 ILE cc_start: 0.9027 (mm) cc_final: 0.8765 (tp) REVERT: Z 85 MET cc_start: 0.8292 (mmt) cc_final: 0.8007 (mmt) REVERT: 7 136 ASP cc_start: 0.7855 (m-30) cc_final: 0.7559 (m-30) REVERT: 7 173 MET cc_start: 0.5145 (pmm) cc_final: 0.4471 (ptp) REVERT: U 81 GLU cc_start: 0.6167 (pp20) cc_final: 0.5962 (mt-10) REVERT: J 2 LEU cc_start: 0.7483 (mt) cc_final: 0.7092 (mt) outliers start: 1 outliers final: 0 residues processed: 493 average time/residue: 0.0800 time to fit residues: 58.0392 Evaluate side-chains 424 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.141523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124021 restraints weight = 23945.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.126373 restraints weight = 15864.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.127804 restraints weight = 11677.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129018 restraints weight = 9502.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.129627 restraints weight = 8111.622| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9599 Z= 0.168 Angle : 0.897 11.554 13029 Z= 0.404 Chirality : 0.046 0.383 1638 Planarity : 0.004 0.050 1561 Dihedral : 22.848 178.556 1704 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.11 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.65 (0.24), residues: 1192 helix: 0.04 (0.16), residues: 995 sheet: None (None), residues: 0 loop : -2.34 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 50 TYR 0.020 0.002 TYR U 82 PHE 0.042 0.002 PHE T 70 TRP 0.023 0.002 TRP U 67 HIS 0.003 0.001 HIS U 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 9599) covalent geometry : angle 0.89731 / 0.40 (13029) hydrogen bonds : bond 0.04055 / 2.69 ( 708) hydrogen bonds : angle 4.38387 / 3.04 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.8018 (tt) cc_final: 0.7151 (mt) REVERT: L 3 LEU cc_start: 0.8639 (tt) cc_final: 0.8238 (mt) REVERT: L 5 LEU cc_start: 0.7387 (pt) cc_final: 0.6733 (mp) REVERT: L 39 ARG cc_start: 0.7756 (ptm-80) cc_final: 0.7365 (tpt170) REVERT: L 67 MET cc_start: 0.6636 (pmm) cc_final: 0.6224 (mmt) REVERT: P 5 LEU cc_start: 0.8224 (pt) cc_final: 0.7489 (pt) REVERT: P 14 ILE cc_start: 0.9244 (pt) cc_final: 0.8823 (mt) REVERT: P 48 PHE cc_start: 0.8365 (t80) cc_final: 0.8153 (t80) REVERT: Q 50 MET cc_start: 0.8452 (ptp) cc_final: 0.8017 (ptt) REVERT: Q 72 LEU cc_start: 0.7369 (tp) cc_final: 0.7148 (tp) REVERT: R 3 LEU cc_start: 0.7087 (tt) cc_final: 0.6246 (mt) REVERT: R 44 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7883 (ptmm) REVERT: S 34 ILE cc_start: 0.9479 (mt) cc_final: 0.9203 (tp) REVERT: S 50 MET cc_start: 0.7286 (mpp) cc_final: 0.7063 (mpp) REVERT: S 68 VAL cc_start: 0.6897 (t) cc_final: 0.6610 (t) REVERT: 8 29 GLN cc_start: 0.8191 (mp10) cc_final: 0.7968 (mp10) REVERT: 8 34 MET cc_start: 0.8150 (ppp) cc_final: 0.7860 (ppp) REVERT: 8 37 ARG cc_start: 0.7857 (ptm160) cc_final: 0.6864 (ptm160) REVERT: 8 39 TYR cc_start: 0.7473 (m-80) cc_final: 0.7167 (m-80) REVERT: X 31 LEU cc_start: 0.8508 (tt) cc_final: 0.7992 (pp) REVERT: X 56 SER cc_start: 0.7874 (m) cc_final: 0.7589 (m) REVERT: X 67 ASP cc_start: 0.7501 (t70) cc_final: 0.7184 (t70) REVERT: X 72 MET cc_start: 0.9254 (tmm) cc_final: 0.8685 (tmm) REVERT: X 81 ASN cc_start: 0.8362 (p0) cc_final: 0.8106 (p0) REVERT: X 84 LEU cc_start: 0.8615 (mp) cc_final: 0.8045 (tp) REVERT: X 98 ILE cc_start: 0.8971 (mm) cc_final: 0.8736 (mm) REVERT: X 232 TYR cc_start: 0.8243 (t80) cc_final: 0.8034 (t80) REVERT: X 236 ILE cc_start: 0.9017 (mm) cc_final: 0.8728 (tp) REVERT: Z 85 MET cc_start: 0.8227 (mmt) cc_final: 0.7969 (mmt) REVERT: 7 173 MET cc_start: 0.5143 (pmm) cc_final: 0.4770 (ptp) REVERT: U 50 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7783 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.0793 time to fit residues: 56.3177 Evaluate side-chains 415 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 3.9990 chunk 113 optimal weight: 0.1980 chunk 84 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 ASN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.139839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121696 restraints weight = 23870.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124320 restraints weight = 15454.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125808 restraints weight = 11102.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.127229 restraints weight = 8957.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.128025 restraints weight = 7481.201| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9599 Z= 0.175 Angle : 0.918 12.841 13029 Z= 0.415 Chirality : 0.047 0.379 1638 Planarity : 0.004 0.054 1561 Dihedral : 21.616 176.714 1704 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.59 (0.24), residues: 1192 helix: 0.06 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -2.23 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 50 TYR 0.033 0.002 TYR U 82 PHE 0.041 0.003 PHE T 70 TRP 0.028 0.002 TRP U 67 HIS 0.003 0.001 HIS U 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 9599) covalent geometry : angle 0.91826 / 0.41 (13029) hydrogen bonds : bond 0.04041 / 2.72 ( 708) hydrogen bonds : angle 4.48895 / 3.12 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.8075 (tt) cc_final: 0.7133 (mt) REVERT: L 3 LEU cc_start: 0.8535 (tt) cc_final: 0.8152 (mt) REVERT: L 5 LEU cc_start: 0.7518 (pt) cc_final: 0.6930 (mp) REVERT: L 39 ARG cc_start: 0.7774 (ptm-80) cc_final: 0.6890 (tmt-80) REVERT: L 40 ASN cc_start: 0.8125 (t0) cc_final: 0.7844 (t0) REVERT: P 2 GLN cc_start: 0.7709 (tp40) cc_final: 0.7246 (tp40) REVERT: P 5 LEU cc_start: 0.8116 (pt) cc_final: 0.7880 (pt) REVERT: P 26 ILE cc_start: 0.9351 (pt) cc_final: 0.8996 (tp) REVERT: Q 50 MET cc_start: 0.8468 (ptp) cc_final: 0.8114 (ptt) REVERT: Q 67 MET cc_start: 0.7509 (tmm) cc_final: 0.7236 (ttm) REVERT: R 3 LEU cc_start: 0.7033 (tt) cc_final: 0.6276 (mt) REVERT: S 34 ILE cc_start: 0.9461 (mt) cc_final: 0.9205 (tp) REVERT: S 50 MET cc_start: 0.7333 (mpp) cc_final: 0.7118 (mpp) REVERT: 8 29 GLN cc_start: 0.8320 (mp10) cc_final: 0.8010 (mp10) REVERT: 8 37 ARG cc_start: 0.8023 (ptm160) cc_final: 0.6932 (ptm160) REVERT: X 31 LEU cc_start: 0.8537 (tt) cc_final: 0.8315 (pp) REVERT: X 67 ASP cc_start: 0.7460 (t70) cc_final: 0.7107 (t70) REVERT: X 72 MET cc_start: 0.9076 (tmm) cc_final: 0.8655 (tmm) REVERT: X 81 ASN cc_start: 0.8272 (p0) cc_final: 0.8055 (p0) REVERT: X 84 LEU cc_start: 0.8493 (mp) cc_final: 0.7958 (tp) REVERT: X 98 ILE cc_start: 0.8916 (mm) cc_final: 0.8605 (mm) REVERT: X 221 MET cc_start: 0.7216 (mmm) cc_final: 0.6932 (mmt) REVERT: Z 66 THR cc_start: 0.7291 (p) cc_final: 0.7042 (p) REVERT: Z 78 LYS cc_start: 0.8563 (tttt) cc_final: 0.8009 (tptm) REVERT: 7 169 ASN cc_start: 0.6009 (p0) cc_final: 0.5700 (p0) REVERT: 7 173 MET cc_start: 0.5185 (pmm) cc_final: 0.4854 (ptp) REVERT: J 2 LEU cc_start: 0.7404 (mt) cc_final: 0.7168 (mt) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.0801 time to fit residues: 56.6016 Evaluate side-chains 407 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 103 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 249 HIS Z 93 ASN U 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.141906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.123972 restraints weight = 23440.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.126535 restraints weight = 15125.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.128139 restraints weight = 10965.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.129436 restraints weight = 8791.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.130209 restraints weight = 7402.237| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9599 Z= 0.159 Angle : 0.926 13.177 13029 Z= 0.414 Chirality : 0.047 0.379 1638 Planarity : 0.004 0.045 1561 Dihedral : 20.853 176.848 1704 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.46 (0.24), residues: 1192 helix: 0.15 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -2.18 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 176 TYR 0.021 0.002 TYR R 9 PHE 0.039 0.002 PHE T 70 TRP 0.035 0.002 TRP X 126 HIS 0.002 0.001 HIS U 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 9599) covalent geometry : angle 0.92551 / 0.41 (13029) hydrogen bonds : bond 0.03921 / 2.62 ( 708) hydrogen bonds : angle 4.40240 / 3.05 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.8166 (tt) cc_final: 0.7348 (mt) REVERT: L 3 LEU cc_start: 0.8572 (tt) cc_final: 0.8175 (mt) REVERT: L 5 LEU cc_start: 0.7462 (pt) cc_final: 0.6809 (mp) REVERT: L 39 ARG cc_start: 0.7771 (ptm-80) cc_final: 0.6866 (tmt-80) REVERT: L 40 ASN cc_start: 0.8092 (t0) cc_final: 0.7776 (t0) REVERT: L 67 MET cc_start: 0.6460 (pmm) cc_final: 0.6237 (mmp) REVERT: M 63 LEU cc_start: 0.8893 (mm) cc_final: 0.8255 (mt) REVERT: P 5 LEU cc_start: 0.8195 (pt) cc_final: 0.7562 (pt) REVERT: P 19 LEU cc_start: 0.7611 (pp) cc_final: 0.7329 (pp) REVERT: P 26 ILE cc_start: 0.9342 (pt) cc_final: 0.9014 (tp) REVERT: Q 50 MET cc_start: 0.8533 (ptp) cc_final: 0.8137 (ptt) REVERT: R 3 LEU cc_start: 0.6957 (tt) cc_final: 0.6139 (mt) REVERT: R 5 LEU cc_start: 0.8153 (pt) cc_final: 0.6980 (pt) REVERT: S 34 ILE cc_start: 0.9426 (mt) cc_final: 0.9202 (tp) REVERT: 8 29 GLN cc_start: 0.8019 (mp10) cc_final: 0.7307 (mp10) REVERT: 8 31 PHE cc_start: 0.7777 (m-80) cc_final: 0.7569 (m-80) REVERT: 8 34 MET cc_start: 0.7997 (ppp) cc_final: 0.7764 (ppp) REVERT: 8 37 ARG cc_start: 0.8191 (ptm160) cc_final: 0.7701 (ptm160) REVERT: 8 39 TYR cc_start: 0.7428 (m-80) cc_final: 0.7205 (m-80) REVERT: X 31 LEU cc_start: 0.8764 (tt) cc_final: 0.8322 (pp) REVERT: X 71 ASN cc_start: 0.7569 (m110) cc_final: 0.7289 (m-40) REVERT: X 72 MET cc_start: 0.9234 (tmm) cc_final: 0.8719 (tmm) REVERT: X 84 LEU cc_start: 0.8530 (mp) cc_final: 0.7865 (tp) REVERT: X 98 ILE cc_start: 0.9028 (mm) cc_final: 0.8722 (mm) REVERT: 7 170 LEU cc_start: 0.9086 (pp) cc_final: 0.8873 (pp) REVERT: 7 173 MET cc_start: 0.5119 (pmm) cc_final: 0.4803 (ptp) REVERT: U 73 ILE cc_start: 0.8162 (tp) cc_final: 0.7944 (tp) REVERT: J 2 LEU cc_start: 0.7462 (mt) cc_final: 0.7260 (mt) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.0811 time to fit residues: 57.4008 Evaluate side-chains 412 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.0000 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 38 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 249 HIS U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.142705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125555 restraints weight = 23371.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.127956 restraints weight = 15241.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129726 restraints weight = 11124.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.130688 restraints weight = 8819.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.131672 restraints weight = 7602.292| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9599 Z= 0.161 Angle : 0.943 14.488 13029 Z= 0.423 Chirality : 0.048 0.383 1638 Planarity : 0.004 0.046 1561 Dihedral : 20.261 178.602 1704 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.69 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.49 (0.24), residues: 1192 helix: 0.13 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -2.19 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 84 TYR 0.024 0.002 TYR P 9 PHE 0.040 0.002 PHE T 70 TRP 0.058 0.003 TRP X 126 HIS 0.002 0.001 HIS X 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 9599) covalent geometry : angle 0.94341 / 0.42 (13029) hydrogen bonds : bond 0.03959 / 2.63 ( 708) hydrogen bonds : angle 4.42609 / 3.07 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.8250 (tt) cc_final: 0.7317 (mt) REVERT: L 3 LEU cc_start: 0.8580 (tt) cc_final: 0.8146 (mt) REVERT: L 5 LEU cc_start: 0.7410 (pt) cc_final: 0.6956 (mp) REVERT: L 39 ARG cc_start: 0.7829 (ptm-80) cc_final: 0.6907 (tmt-80) REVERT: L 40 ASN cc_start: 0.8037 (t0) cc_final: 0.7713 (t0) REVERT: L 67 MET cc_start: 0.6528 (pmm) cc_final: 0.6274 (mmp) REVERT: M 63 LEU cc_start: 0.8967 (mm) cc_final: 0.8584 (mt) REVERT: P 2 GLN cc_start: 0.7712 (tp40) cc_final: 0.6086 (pm20) REVERT: P 5 LEU cc_start: 0.8116 (pt) cc_final: 0.7882 (pt) REVERT: P 19 LEU cc_start: 0.7634 (pp) cc_final: 0.7383 (pp) REVERT: P 26 ILE cc_start: 0.9270 (pt) cc_final: 0.9022 (tp) REVERT: Q 47 VAL cc_start: 0.8659 (p) cc_final: 0.8223 (p) REVERT: Q 50 MET cc_start: 0.8505 (ptp) cc_final: 0.8148 (ptt) REVERT: R 2 GLN cc_start: 0.5892 (pm20) cc_final: 0.5569 (pm20) REVERT: R 3 LEU cc_start: 0.6936 (tt) cc_final: 0.6258 (mt) REVERT: R 5 LEU cc_start: 0.8359 (pt) cc_final: 0.7220 (pt) REVERT: S 34 ILE cc_start: 0.9474 (mt) cc_final: 0.9196 (tp) REVERT: T 39 ARG cc_start: 0.9009 (ptm160) cc_final: 0.8702 (ptp90) REVERT: 8 29 GLN cc_start: 0.8025 (mp10) cc_final: 0.7348 (mp10) REVERT: 8 34 MET cc_start: 0.8193 (ppp) cc_final: 0.7902 (ppp) REVERT: 8 37 ARG cc_start: 0.8171 (ptm160) cc_final: 0.7661 (ptm160) REVERT: X 31 LEU cc_start: 0.8706 (tt) cc_final: 0.8315 (pp) REVERT: X 72 MET cc_start: 0.9152 (tmm) cc_final: 0.8676 (tmm) REVERT: X 84 LEU cc_start: 0.8579 (mp) cc_final: 0.7910 (tp) REVERT: X 98 ILE cc_start: 0.9035 (mm) cc_final: 0.8765 (mm) REVERT: X 233 VAL cc_start: 0.9032 (t) cc_final: 0.8796 (t) REVERT: 7 173 MET cc_start: 0.4961 (pmm) cc_final: 0.4645 (ptp) outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.0799 time to fit residues: 56.1555 Evaluate side-chains 408 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 249 HIS 7 169 ASN U 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123731 restraints weight = 23688.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.126075 restraints weight = 15699.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127672 restraints weight = 11535.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.128842 restraints weight = 9247.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.129177 restraints weight = 7859.995| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9599 Z= 0.186 Angle : 0.958 12.604 13029 Z= 0.438 Chirality : 0.048 0.381 1638 Planarity : 0.004 0.046 1561 Dihedral : 19.981 179.897 1704 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.52 (0.25), residues: 1192 helix: 0.13 (0.17), residues: 997 sheet: None (None), residues: 0 loop : -2.31 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 39 TYR 0.021 0.002 TYR R 9 PHE 0.053 0.003 PHE T 70 TRP 0.041 0.003 TRP X 126 HIS 0.003 0.001 HIS U 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 9599) covalent geometry : angle 0.95802 / 0.44 (13029) hydrogen bonds : bond 0.04088 / 2.72 ( 708) hydrogen bonds : angle 4.60962 / 3.20 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.8246 (tt) cc_final: 0.7164 (mt) REVERT: L 3 LEU cc_start: 0.8593 (tt) cc_final: 0.8109 (mp) REVERT: L 5 LEU cc_start: 0.7414 (pt) cc_final: 0.6930 (mp) REVERT: L 39 ARG cc_start: 0.7817 (ptm-80) cc_final: 0.6872 (tmt-80) REVERT: L 40 ASN cc_start: 0.8065 (t0) cc_final: 0.7709 (t0) REVERT: L 67 MET cc_start: 0.6722 (pmm) cc_final: 0.6271 (mmp) REVERT: O 67 MET cc_start: 0.7598 (ptt) cc_final: 0.7349 (ptt) REVERT: P 2 GLN cc_start: 0.7773 (tp40) cc_final: 0.7568 (tp-100) REVERT: P 5 LEU cc_start: 0.8217 (pt) cc_final: 0.7496 (pt) REVERT: Q 17 ILE cc_start: 0.7919 (pt) cc_final: 0.7599 (pt) REVERT: Q 50 MET cc_start: 0.8560 (ptp) cc_final: 0.8170 (ptt) REVERT: Q 72 LEU cc_start: 0.7166 (tp) cc_final: 0.6929 (tp) REVERT: R 3 LEU cc_start: 0.6910 (tt) cc_final: 0.6106 (mt) REVERT: R 5 LEU cc_start: 0.8028 (pt) cc_final: 0.6722 (pt) REVERT: S 34 ILE cc_start: 0.9475 (mt) cc_final: 0.9236 (tp) REVERT: T 39 ARG cc_start: 0.8937 (ptm160) cc_final: 0.8590 (ptp90) REVERT: T 48 PHE cc_start: 0.7422 (t80) cc_final: 0.6843 (t80) REVERT: 8 29 GLN cc_start: 0.8152 (mp10) cc_final: 0.7568 (mp10) REVERT: 8 34 MET cc_start: 0.8302 (ppp) cc_final: 0.7947 (ppp) REVERT: 8 37 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7576 (ptm160) REVERT: X 31 LEU cc_start: 0.8653 (tt) cc_final: 0.8316 (pp) REVERT: X 72 MET cc_start: 0.9112 (tmm) cc_final: 0.8720 (tmm) REVERT: X 84 LEU cc_start: 0.8368 (mp) cc_final: 0.7866 (tp) REVERT: X 98 ILE cc_start: 0.9036 (mm) cc_final: 0.8702 (mm) REVERT: X 232 TYR cc_start: 0.8180 (t80) cc_final: 0.7972 (t80) REVERT: X 234 TRP cc_start: 0.7862 (t-100) cc_final: 0.7545 (t-100) REVERT: 7 173 MET cc_start: 0.5208 (pmm) cc_final: 0.4798 (ptp) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.0795 time to fit residues: 54.6781 Evaluate side-chains 404 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 73 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 ASN 7 169 ASN U 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.141945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.123876 restraints weight = 23616.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126529 restraints weight = 15335.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.128125 restraints weight = 11144.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129432 restraints weight = 8993.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.130166 restraints weight = 7611.461| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9599 Z= 0.169 Angle : 0.955 14.517 13029 Z= 0.431 Chirality : 0.048 0.376 1638 Planarity : 0.004 0.044 1561 Dihedral : 19.567 178.699 1704 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.47 (0.24), residues: 1192 helix: 0.14 (0.17), residues: 998 sheet: None (None), residues: 0 loop : -2.17 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 39 TYR 0.036 0.002 TYR U 82 PHE 0.027 0.002 PHE U 56 TRP 0.045 0.003 TRP X 126 HIS 0.002 0.001 HIS X 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 9599) covalent geometry : angle 0.95525 / 0.43 (13029) hydrogen bonds : bond 0.04075 / 2.73 ( 708) hydrogen bonds : angle 4.62650 / 3.21 ( 2112) =============================================================================== Job complete usr+sys time: 1848.79 seconds wall clock time: 32 minutes 46.90 seconds (1966.90 seconds total)