Starting phenix.real_space_refine on Sun Jul 27 06:29:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cp5_7547/07_2025/6cp5_7547.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cp5_7547/07_2025/6cp5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6cp5_7547/07_2025/6cp5_7547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cp5_7547/07_2025/6cp5_7547.map" model { file = "/net/cci-nas-00/data/ceres_data/6cp5_7547/07_2025/6cp5_7547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cp5_7547/07_2025/6cp5_7547.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS: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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 1, 'ARG:plan': 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: 6.76, per 1000 atoms: 0.72 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: 2.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.88 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: 2.42 Time building geometry restraints manager: 3.27 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.340 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP U 67 HIS 0.003 0.001 HIS U 68 PHE 0.020 0.001 PHE O 70 TYR 0.014 0.001 TYR J 25 ARG 0.001 0.000 ARG X 57 Details of bonding type rmsd hydrogen bonds : bond 0.18812 ( 708) hydrogen bonds : angle 7.67507 ( 2112) covalent geometry : bond 0.00430 ( 9599) covalent geometry : angle 0.90677 (13029) *********************** 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 : 0.901 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: K 43 ILE cc_start: 0.8845 (tp) cc_final: 0.8623 (tp) REVERT: K 67 MET cc_start: 0.8852 (ttp) cc_final: 0.8573 (ttm) REVERT: L 5 LEU cc_start: 0.7455 (pt) cc_final: 0.6755 (mp) REVERT: L 39 ARG cc_start: 0.7325 (ptm-80) cc_final: 0.6999 (tpt170) REVERT: L 47 VAL cc_start: 0.9000 (t) cc_final: 0.8773 (p) REVERT: L 67 MET cc_start: 0.7773 (pp-130) cc_final: 0.7317 (tpt) REVERT: L 68 VAL cc_start: 0.7931 (t) cc_final: 0.7692 (t) REVERT: M 44 LYS cc_start: 0.8549 (ttmt) cc_final: 0.7909 (tptp) REVERT: M 52 ILE cc_start: 0.8649 (tt) cc_final: 0.8437 (tt) REVERT: M 67 MET cc_start: 0.8672 (pp-130) cc_final: 0.8310 (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: 0.7883 (pt) REVERT: Q 38 SER cc_start: 0.8386 (p) cc_final: 0.7921 (m) REVERT: R 3 LEU cc_start: 0.6898 (tm) cc_final: 0.6045 (mt) REVERT: R 5 LEU cc_start: 0.8290 (pt) cc_final: 0.7105 (pt) REVERT: R 26 ILE cc_start: 0.8506 (pt) cc_final: 0.7836 (mt) REVERT: S 43 ILE cc_start: 0.8345 (tt) cc_final: 0.8129 (tp) REVERT: 8 26 LEU cc_start: 0.8733 (tt) cc_final: 0.8311 (tt) REVERT: X 31 LEU cc_start: 0.8573 (tt) cc_final: 0.8183 (pp) REVERT: X 56 SER cc_start: 0.7112 (m) cc_final: 0.6817 (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: 0.8147 (tp) REVERT: X 92 LEU cc_start: 0.8662 (mt) cc_final: 0.8037 (mt) REVERT: X 98 ILE cc_start: 0.8619 (mm) cc_final: 0.8394 (mm) REVERT: X 120 SER cc_start: 0.8715 (t) cc_final: 0.8507 (p) REVERT: X 164 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6456 (pp) REVERT: X 190 ILE cc_start: 0.7885 (mt) cc_final: 0.7526 (mm) REVERT: 7 128 ARG cc_start: 0.6699 (ttm170) cc_final: 0.6446 (ttm-80) REVERT: 7 148 LYS cc_start: 0.7935 (tttp) cc_final: 0.6732 (ttmt) REVERT: U 32 LYS cc_start: 0.5617 (ttmt) cc_final: 0.5359 (ttpt) REVERT: U 68 HIS cc_start: 0.7759 (m-70) cc_final: 0.7341 (t-170) REVERT: J 1 MET cc_start: 0.6384 (ttp) cc_final: 0.5484 (mtt) outliers start: 21 outliers final: 12 residues processed: 625 average time/residue: 0.1940 time to fit residues: 170.3290 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 : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 185 HIS ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.145028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.127358 restraints weight = 23230.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129708 restraints weight = 15564.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.131329 restraints weight = 11588.705| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9599 Z= 0.168 Angle : 0.882 14.124 13029 Z= 0.392 Chirality : 0.046 0.317 1638 Planarity : 0.005 0.051 1561 Dihedral : 30.470 179.788 1704 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 0.32 % Allowed : 4.90 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.22), residues: 1192 helix: -1.16 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -2.82 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 126 HIS 0.006 0.001 HIS U 68 PHE 0.048 0.002 PHE O 64 TYR 0.022 0.002 TYR U 78 ARG 0.010 0.001 ARG 8 37 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 708) hydrogen bonds : angle 4.94046 ( 2112) covalent geometry : bond 0.00367 ( 9599) covalent geometry : angle 0.88150 (13029) *********************** 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 522 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 519 time to evaluate : 0.962 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: K 53 LEU cc_start: 0.7933 (tt) cc_final: 0.7328 (mt) REVERT: K 63 LEU cc_start: 0.7959 (mt) cc_final: 0.7635 (mt) REVERT: L 3 LEU cc_start: 0.8776 (tt) cc_final: 0.8462 (mp) REVERT: L 5 LEU cc_start: 0.7365 (pt) cc_final: 0.6865 (mp) REVERT: L 39 ARG cc_start: 0.7504 (ptm-80) cc_final: 0.7106 (tpt170) REVERT: L 47 VAL cc_start: 0.8767 (t) cc_final: 0.8512 (p) REVERT: L 50 MET cc_start: 0.7897 (ppp) cc_final: 0.7695 (ppp) REVERT: O 14 ILE cc_start: 0.8168 (pt) cc_final: 0.7891 (pt) REVERT: P 2 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7624 (tp40) REVERT: P 5 LEU cc_start: 0.8365 (pt) cc_final: 0.7466 (pt) REVERT: P 44 LYS cc_start: 0.7953 (tptt) cc_final: 0.7629 (tptt) REVERT: Q 2 GLN cc_start: 0.7714 (mp10) cc_final: 0.7434 (mp10) REVERT: Q 5 LEU cc_start: 0.8368 (pt) cc_final: 0.7179 (mp) REVERT: Q 30 PHE cc_start: 0.8211 (m-80) cc_final: 0.7929 (m-80) REVERT: Q 48 PHE cc_start: 0.8061 (t80) cc_final: 0.7611 (t80) REVERT: Q 50 MET cc_start: 0.8730 (ptp) cc_final: 0.8502 (ptm) REVERT: Q 52 ILE cc_start: 0.8006 (tt) cc_final: 0.7641 (mm) REVERT: R 3 LEU cc_start: 0.6949 (tt) cc_final: 0.6159 (mt) REVERT: R 5 LEU cc_start: 0.8223 (pt) cc_final: 0.7051 (pt) REVERT: R 26 ILE cc_start: 0.8469 (pt) cc_final: 0.7717 (mt) REVERT: R 43 ILE cc_start: 0.9012 (tt) cc_final: 0.8755 (tt) REVERT: R 64 PHE cc_start: 0.7970 (m-10) cc_final: 0.7593 (m-10) REVERT: S 43 ILE cc_start: 0.8226 (tt) cc_final: 0.7819 (tp) REVERT: S 57 LEU cc_start: 0.8777 (mt) cc_final: 0.8440 (mt) REVERT: S 66 LEU cc_start: 0.8138 (pt) cc_final: 0.7687 (tt) REVERT: 8 10 MET cc_start: 0.6694 (mmp) cc_final: 0.5487 (mpp) REVERT: 8 34 MET cc_start: 0.8187 (ppp) cc_final: 0.7961 (ppp) REVERT: 8 37 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7650 (ptm160) REVERT: X 31 LEU cc_start: 0.8645 (tt) cc_final: 0.8041 (pp) REVERT: X 72 MET cc_start: 0.8865 (tmm) cc_final: 0.8369 (tmm) REVERT: X 81 ASN cc_start: 0.8341 (p0) cc_final: 0.8106 (p0) REVERT: X 84 LEU cc_start: 0.8662 (mp) cc_final: 0.8133 (tp) REVERT: X 92 LEU cc_start: 0.8465 (mt) cc_final: 0.7951 (mt) REVERT: X 104 MET cc_start: 0.7891 (tpt) cc_final: 0.7611 (tpt) REVERT: X 120 SER cc_start: 0.8607 (t) cc_final: 0.8319 (p) REVERT: X 190 ILE cc_start: 0.7971 (mt) cc_final: 0.7502 (mm) REVERT: X 223 GLU cc_start: 0.8925 (tp30) cc_final: 0.8523 (tp30) REVERT: X 224 PHE cc_start: 0.7414 (t80) cc_final: 0.7199 (t80) REVERT: X 236 ILE cc_start: 0.8940 (mm) cc_final: 0.8518 (tp) REVERT: Z 78 LYS cc_start: 0.8453 (tttt) cc_final: 0.7998 (tptp) REVERT: 7 116 ASP cc_start: 0.8022 (t0) cc_final: 0.7760 (m-30) REVERT: 7 128 ARG cc_start: 0.6937 (ttm170) cc_final: 0.6727 (ttm-80) REVERT: 7 130 PHE cc_start: 0.6999 (p90) cc_final: 0.6672 (p90) REVERT: 7 173 MET cc_start: 0.5004 (pmm) cc_final: 0.4387 (pmm) REVERT: U 50 ARG cc_start: 0.8123 (mpt-90) cc_final: 0.7853 (mpp80) REVERT: J 2 LEU cc_start: 0.7402 (mt) cc_final: 0.6946 (mt) REVERT: J 27 MET cc_start: 0.7800 (tpp) cc_final: 0.7230 (tmm) outliers start: 3 outliers final: 0 residues processed: 521 average time/residue: 0.2457 time to fit residues: 182.2295 Evaluate side-chains 428 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.142487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124861 restraints weight = 23836.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127591 restraints weight = 16969.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.129512 restraints weight = 11331.841| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9599 Z= 0.165 Angle : 0.838 11.128 13029 Z= 0.381 Chirality : 0.045 0.369 1638 Planarity : 0.004 0.050 1561 Dihedral : 28.002 178.696 1704 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.69 % Favored : 96.14 % Rotamer: Outliers : 0.53 % Allowed : 6.82 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 1192 helix: -0.44 (0.16), residues: 998 sheet: None (None), residues: 0 loop : -2.58 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP X 126 HIS 0.005 0.001 HIS U 68 PHE 0.042 0.002 PHE T 70 TYR 0.023 0.002 TYR X 241 ARG 0.002 0.000 ARG 8 42 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 708) hydrogen bonds : angle 4.57171 ( 2112) covalent geometry : bond 0.00384 ( 9599) covalent geometry : angle 0.83816 (13029) *********************** 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 504 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 499 time to evaluate : 1.042 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: 0.8061 (tt) cc_final: 0.7311 (mt) REVERT: L 3 LEU cc_start: 0.8749 (tt) cc_final: 0.8388 (mt) REVERT: L 5 LEU cc_start: 0.7489 (pt) cc_final: 0.7126 (mp) REVERT: L 39 ARG cc_start: 0.7749 (ptm-80) cc_final: 0.6902 (tmt-80) REVERT: L 40 ASN cc_start: 0.7892 (t0) cc_final: 0.7557 (t0) REVERT: L 47 VAL cc_start: 0.9006 (t) cc_final: 0.8588 (p) REVERT: M 43 ILE cc_start: 0.8911 (tp) cc_final: 0.8614 (tt) REVERT: M 52 ILE cc_start: 0.8219 (tt) cc_final: 0.7994 (tp) REVERT: P 5 LEU cc_start: 0.8194 (pt) cc_final: 0.7938 (pt) REVERT: Q 5 LEU cc_start: 0.8329 (pt) cc_final: 0.7271 (mp) REVERT: Q 48 PHE cc_start: 0.8116 (t80) cc_final: 0.7845 (t80) REVERT: Q 50 MET cc_start: 0.8666 (ptp) cc_final: 0.8461 (ptm) REVERT: Q 67 MET cc_start: 0.7560 (ptm) cc_final: 0.7149 (tmm) REVERT: R 3 LEU cc_start: 0.7051 (tt) cc_final: 0.6180 (mt) REVERT: R 5 LEU cc_start: 0.8054 (pt) cc_final: 0.7259 (pt) REVERT: R 43 ILE cc_start: 0.8935 (tt) cc_final: 0.8676 (tt) REVERT: R 64 PHE cc_start: 0.7818 (m-10) cc_final: 0.7488 (m-10) REVERT: S 43 ILE cc_start: 0.8384 (tt) cc_final: 0.7837 (mm) REVERT: S 46 THR cc_start: 0.8803 (m) cc_final: 0.8505 (m) REVERT: S 47 VAL cc_start: 0.9096 (t) cc_final: 0.8846 (t) REVERT: S 57 LEU cc_start: 0.8538 (mt) cc_final: 0.8209 (mt) REVERT: T 4 VAL cc_start: 0.7802 (t) cc_final: 0.7392 (t) REVERT: 8 10 MET cc_start: 0.6865 (mmp) cc_final: 0.5601 (mpp) REVERT: 8 31 PHE cc_start: 0.7943 (m-80) cc_final: 0.7652 (m-80) REVERT: 8 34 MET cc_start: 0.8163 (ppp) cc_final: 0.7665 (ppp) REVERT: 8 35 ILE cc_start: 0.9384 (mt) cc_final: 0.9062 (mm) REVERT: 8 37 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7550 (ptm160) REVERT: X 31 LEU cc_start: 0.8467 (tt) cc_final: 0.8007 (pp) REVERT: X 54 ILE cc_start: 0.8486 (mm) cc_final: 0.8225 (mm) REVERT: X 72 MET cc_start: 0.8956 (tmm) cc_final: 0.8547 (tmm) REVERT: X 81 ASN cc_start: 0.8254 (p0) cc_final: 0.8032 (p0) REVERT: X 84 LEU cc_start: 0.8584 (mp) cc_final: 0.8183 (tp) REVERT: X 88 MET cc_start: 0.8017 (tpt) cc_final: 0.7700 (tpt) REVERT: X 92 LEU cc_start: 0.8445 (mt) cc_final: 0.7920 (mt) REVERT: X 98 ILE cc_start: 0.9037 (mm) cc_final: 0.8756 (mm) REVERT: X 190 ILE cc_start: 0.7847 (mt) cc_final: 0.7646 (mm) REVERT: X 236 ILE cc_start: 0.8950 (mm) cc_final: 0.8593 (tp) REVERT: Z 66 THR cc_start: 0.7309 (p) cc_final: 0.7063 (p) REVERT: Z 93 ASN cc_start: 0.8175 (m-40) cc_final: 0.7858 (m-40) REVERT: 7 112 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7755 (pttm) REVERT: 7 116 ASP cc_start: 0.8059 (t0) cc_final: 0.7793 (m-30) REVERT: 7 128 ARG cc_start: 0.6951 (ttm170) cc_final: 0.6433 (ttm-80) REVERT: 7 131 ASP cc_start: 0.8830 (t0) cc_final: 0.8421 (t0) REVERT: 7 173 MET cc_start: 0.5327 (pmm) cc_final: 0.4788 (pmm) REVERT: J 27 MET cc_start: 0.7757 (tpp) cc_final: 0.7218 (tmm) outliers start: 5 outliers final: 0 residues processed: 502 average time/residue: 0.1945 time to fit residues: 139.5897 Evaluate side-chains 420 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 46 optimal weight: 0.0040 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 129 ASN U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124869 restraints weight = 23692.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127499 restraints weight = 15406.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129221 restraints weight = 11170.591| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9599 Z= 0.158 Angle : 0.865 12.263 13029 Z= 0.388 Chirality : 0.046 0.379 1638 Planarity : 0.004 0.063 1561 Dihedral : 26.005 177.675 1704 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 0.32 % Allowed : 4.69 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1192 helix: -0.20 (0.16), residues: 998 sheet: None (None), residues: 0 loop : -2.41 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP X 126 HIS 0.003 0.001 HIS X 114 PHE 0.029 0.002 PHE Q 64 TYR 0.029 0.002 TYR U 55 ARG 0.005 0.000 ARG U 50 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 708) hydrogen bonds : angle 4.45182 ( 2112) covalent geometry : bond 0.00361 ( 9599) covalent geometry : angle 0.86532 (13029) *********************** 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 504 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 501 time to evaluate : 1.199 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: L 3 LEU cc_start: 0.8693 (tt) cc_final: 0.8351 (mt) REVERT: L 5 LEU cc_start: 0.7382 (pt) cc_final: 0.6804 (mp) REVERT: L 39 ARG cc_start: 0.7675 (ptm-80) cc_final: 0.6911 (tmt-80) REVERT: L 40 ASN cc_start: 0.7797 (t0) cc_final: 0.7397 (t0) REVERT: L 47 VAL cc_start: 0.8907 (t) cc_final: 0.8402 (p) REVERT: L 67 MET cc_start: 0.8013 (ptt) cc_final: 0.7654 (ptp) REVERT: M 52 ILE cc_start: 0.8260 (tt) cc_final: 0.8007 (tp) REVERT: P 2 GLN cc_start: 0.7740 (tp40) cc_final: 0.7387 (tp40) REVERT: P 5 LEU cc_start: 0.8230 (pt) cc_final: 0.7488 (pt) REVERT: P 19 LEU cc_start: 0.7747 (pp) cc_final: 0.7304 (pp) REVERT: Q 5 LEU cc_start: 0.8305 (pt) cc_final: 0.7243 (mp) REVERT: Q 48 PHE cc_start: 0.7970 (t80) cc_final: 0.7748 (t80) REVERT: Q 50 MET cc_start: 0.8603 (ptp) cc_final: 0.8378 (ptm) REVERT: Q 64 PHE cc_start: 0.7132 (m-80) cc_final: 0.6668 (m-80) REVERT: Q 67 MET cc_start: 0.7456 (ptm) cc_final: 0.7180 (tmm) REVERT: R 3 LEU cc_start: 0.6926 (tt) cc_final: 0.6320 (mt) REVERT: R 5 LEU cc_start: 0.8227 (pt) cc_final: 0.7057 (pt) REVERT: S 34 ILE cc_start: 0.9443 (mt) cc_final: 0.9160 (tp) REVERT: S 46 THR cc_start: 0.8796 (m) cc_final: 0.8403 (p) REVERT: 8 25 ILE cc_start: 0.8897 (mt) cc_final: 0.8369 (mt) REVERT: 8 29 GLN cc_start: 0.8657 (mp10) cc_final: 0.7982 (mp10) REVERT: 8 31 PHE cc_start: 0.8074 (m-80) cc_final: 0.7819 (m-80) REVERT: 8 34 MET cc_start: 0.7987 (ppp) cc_final: 0.7415 (ppp) REVERT: 8 35 ILE cc_start: 0.9403 (mt) cc_final: 0.9130 (mm) REVERT: 8 37 ARG cc_start: 0.8177 (ptm160) cc_final: 0.7456 (ptm160) REVERT: X 31 LEU cc_start: 0.8536 (tt) cc_final: 0.8015 (pp) REVERT: X 54 ILE cc_start: 0.8527 (mm) cc_final: 0.8286 (mm) REVERT: X 72 MET cc_start: 0.8928 (tmm) cc_final: 0.8487 (tmm) REVERT: X 81 ASN cc_start: 0.8284 (p0) cc_final: 0.8050 (p0) REVERT: X 84 LEU cc_start: 0.8673 (mp) cc_final: 0.8178 (tp) REVERT: X 88 MET cc_start: 0.8008 (tpt) cc_final: 0.7675 (tpt) REVERT: X 92 LEU cc_start: 0.8590 (mt) cc_final: 0.8148 (mt) REVERT: X 98 ILE cc_start: 0.8959 (mm) cc_final: 0.8734 (mm) REVERT: X 190 ILE cc_start: 0.8004 (mt) cc_final: 0.7712 (mm) REVERT: X 236 ILE cc_start: 0.8971 (mm) cc_final: 0.8649 (tp) REVERT: Z 71 LYS cc_start: 0.6564 (mmtt) cc_final: 0.5377 (tmtt) REVERT: 7 112 LYS cc_start: 0.8209 (tmtt) cc_final: 0.7700 (pttm) REVERT: 7 116 ASP cc_start: 0.8164 (t0) cc_final: 0.7822 (m-30) REVERT: 7 169 ASN cc_start: 0.5861 (t0) cc_final: 0.4044 (t0) REVERT: U 66 LEU cc_start: 0.8893 (mt) cc_final: 0.8573 (pp) REVERT: U 81 GLU cc_start: 0.6021 (pp20) cc_final: 0.5716 (mt-10) REVERT: J 2 LEU cc_start: 0.7481 (mt) cc_final: 0.7275 (mt) outliers start: 3 outliers final: 0 residues processed: 502 average time/residue: 0.2605 time to fit residues: 190.4974 Evaluate side-chains 419 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 27 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** 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 = 0.4019 r_free = 0.4019 target = 0.143533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.125013 restraints weight = 23681.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.127631 restraints weight = 15399.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129282 restraints weight = 11156.407| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9599 Z= 0.157 Angle : 0.864 11.460 13029 Z= 0.388 Chirality : 0.045 0.388 1638 Planarity : 0.004 0.052 1561 Dihedral : 24.225 178.704 1704 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.47 % Rotamer: Outliers : 0.21 % Allowed : 4.48 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1192 helix: -0.06 (0.16), residues: 994 sheet: None (None), residues: 0 loop : -2.43 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP U 67 HIS 0.003 0.001 HIS U 68 PHE 0.044 0.002 PHE T 70 TYR 0.025 0.002 TYR R 9 ARG 0.008 0.001 ARG U 50 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 708) hydrogen bonds : angle 4.39912 ( 2112) covalent geometry : bond 0.00361 ( 9599) covalent geometry : angle 0.86369 (13029) *********************** 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 495 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 1.206 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: 0.7898 (tt) cc_final: 0.7150 (mt) REVERT: L 3 LEU cc_start: 0.8619 (tt) cc_final: 0.8210 (mt) REVERT: L 5 LEU cc_start: 0.7509 (pt) cc_final: 0.6960 (mp) REVERT: L 39 ARG cc_start: 0.7734 (ptm-80) cc_final: 0.7206 (tpt170) REVERT: L 40 ASN cc_start: 0.7894 (t0) cc_final: 0.7471 (t0) REVERT: L 47 VAL cc_start: 0.8841 (t) cc_final: 0.8544 (p) REVERT: L 67 MET cc_start: 0.7955 (ptt) cc_final: 0.7610 (ptt) REVERT: O 67 MET cc_start: 0.7708 (ptt) cc_final: 0.7507 (ptt) REVERT: P 2 GLN cc_start: 0.7838 (tp40) cc_final: 0.7422 (tp40) REVERT: P 5 LEU cc_start: 0.8160 (pt) cc_final: 0.7956 (pt) REVERT: Q 5 LEU cc_start: 0.8245 (pt) cc_final: 0.7273 (mp) REVERT: Q 50 MET cc_start: 0.8436 (ptp) cc_final: 0.7817 (ptt) REVERT: Q 67 MET cc_start: 0.7397 (ptm) cc_final: 0.6958 (tmm) REVERT: R 2 GLN cc_start: 0.6377 (pm20) cc_final: 0.6157 (pm20) REVERT: R 3 LEU cc_start: 0.7087 (tt) cc_final: 0.6231 (mt) REVERT: R 5 LEU cc_start: 0.8113 (pt) cc_final: 0.7346 (pt) REVERT: S 34 ILE cc_start: 0.9466 (mt) cc_final: 0.9170 (tp) REVERT: S 43 ILE cc_start: 0.8369 (tt) cc_final: 0.7664 (mm) REVERT: T 39 ARG cc_start: 0.8846 (ptm160) cc_final: 0.8646 (ptp90) REVERT: 8 25 ILE cc_start: 0.8967 (mt) cc_final: 0.8698 (mt) REVERT: 8 29 GLN cc_start: 0.8497 (mp10) cc_final: 0.8120 (mp10) REVERT: 8 34 MET cc_start: 0.8150 (ppp) cc_final: 0.7773 (ppp) REVERT: 8 35 ILE cc_start: 0.9435 (mt) cc_final: 0.9145 (mm) REVERT: 8 37 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7664 (ptm160) REVERT: X 31 LEU cc_start: 0.8562 (tt) cc_final: 0.7993 (pp) REVERT: X 72 MET cc_start: 0.9080 (tmm) cc_final: 0.8460 (tmm) REVERT: X 84 LEU cc_start: 0.8679 (mp) cc_final: 0.8132 (tp) REVERT: X 98 ILE cc_start: 0.9015 (mm) cc_final: 0.8801 (mm) REVERT: X 236 ILE cc_start: 0.9008 (mm) cc_final: 0.8772 (tp) REVERT: Z 71 LYS cc_start: 0.6533 (mmtt) cc_final: 0.5401 (tmtt) REVERT: 7 136 ASP cc_start: 0.7715 (m-30) cc_final: 0.7512 (m-30) REVERT: 7 169 ASN cc_start: 0.6136 (t0) cc_final: 0.4921 (t0) REVERT: U 66 LEU cc_start: 0.8844 (mt) cc_final: 0.8569 (pp) outliers start: 2 outliers final: 0 residues processed: 494 average time/residue: 0.3038 time to fit residues: 219.6542 Evaluate side-chains 422 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.142536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124574 restraints weight = 23670.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.127120 restraints weight = 15297.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.128816 restraints weight = 11065.525| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9599 Z= 0.158 Angle : 0.885 11.883 13029 Z= 0.395 Chirality : 0.045 0.388 1638 Planarity : 0.004 0.052 1561 Dihedral : 22.993 178.574 1704 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.28 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1192 helix: 0.03 (0.16), residues: 994 sheet: None (None), residues: 0 loop : -2.46 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 67 HIS 0.003 0.001 HIS U 68 PHE 0.046 0.002 PHE T 70 TYR 0.019 0.002 TYR X 241 ARG 0.007 0.001 ARG U 50 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 708) hydrogen bonds : angle 4.37503 ( 2112) covalent geometry : bond 0.00373 ( 9599) covalent geometry : angle 0.88469 (13029) *********************** 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 486 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.053 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: 0.7857 (tt) cc_final: 0.7137 (mt) REVERT: L 3 LEU cc_start: 0.8655 (tt) cc_final: 0.8239 (mt) REVERT: L 5 LEU cc_start: 0.7306 (pt) cc_final: 0.6526 (mp) REVERT: L 39 ARG cc_start: 0.7638 (ptm-80) cc_final: 0.7320 (tpt170) REVERT: L 47 VAL cc_start: 0.8896 (t) cc_final: 0.8540 (p) REVERT: L 67 MET cc_start: 0.7894 (ptt) cc_final: 0.7630 (ptt) REVERT: P 2 GLN cc_start: 0.7834 (tp40) cc_final: 0.7431 (tp40) REVERT: P 5 LEU cc_start: 0.8237 (pt) cc_final: 0.7631 (pt) REVERT: Q 50 MET cc_start: 0.8444 (ptp) cc_final: 0.7876 (ptt) REVERT: Q 67 MET cc_start: 0.7114 (ptm) cc_final: 0.6874 (tmm) REVERT: R 3 LEU cc_start: 0.7063 (tt) cc_final: 0.6209 (mt) REVERT: R 5 LEU cc_start: 0.8285 (pt) cc_final: 0.7084 (pt) REVERT: R 59 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7692 (tt0) REVERT: S 34 ILE cc_start: 0.9461 (mt) cc_final: 0.9201 (tp) REVERT: T 39 ARG cc_start: 0.8893 (ptm160) cc_final: 0.8583 (ptp90) REVERT: 8 34 MET cc_start: 0.8121 (ppp) cc_final: 0.7711 (ppp) REVERT: 8 37 ARG cc_start: 0.8138 (ptm160) cc_final: 0.7701 (ptm160) REVERT: X 31 LEU cc_start: 0.8566 (tt) cc_final: 0.8090 (pp) REVERT: X 32 TYR cc_start: 0.6311 (m-10) cc_final: 0.6111 (m-80) REVERT: X 72 MET cc_start: 0.9119 (tmm) cc_final: 0.8495 (tmm) REVERT: X 81 ASN cc_start: 0.8318 (p0) cc_final: 0.8117 (p0) REVERT: X 84 LEU cc_start: 0.8698 (mp) cc_final: 0.8158 (tp) REVERT: X 98 ILE cc_start: 0.9006 (mm) cc_final: 0.8758 (mm) REVERT: X 221 MET cc_start: 0.7681 (mmp) cc_final: 0.7440 (mmm) REVERT: X 236 ILE cc_start: 0.9076 (mm) cc_final: 0.8798 (tp) REVERT: Z 66 THR cc_start: 0.7173 (p) cc_final: 0.6967 (p) REVERT: 7 116 ASP cc_start: 0.8130 (t0) cc_final: 0.7838 (m-30) REVERT: U 50 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: U 66 LEU cc_start: 0.8856 (mt) cc_final: 0.8602 (pp) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.1910 time to fit residues: 133.7666 Evaluate side-chains 423 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.142116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124494 restraints weight = 24274.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126841 restraints weight = 16050.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.128526 restraints weight = 11824.031| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9599 Z= 0.166 Angle : 0.907 12.355 13029 Z= 0.407 Chirality : 0.046 0.390 1638 Planarity : 0.004 0.048 1561 Dihedral : 21.943 176.875 1704 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1192 helix: 0.06 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -2.26 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP X 126 HIS 0.003 0.001 HIS U 29 PHE 0.042 0.002 PHE T 70 TYR 0.024 0.002 TYR R 9 ARG 0.006 0.001 ARG U 50 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 708) hydrogen bonds : angle 4.40512 ( 2112) covalent geometry : bond 0.00399 ( 9599) covalent geometry : angle 0.90660 (13029) *********************** 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 474 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 1.060 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: 0.8068 (tt) cc_final: 0.7246 (mt) REVERT: L 3 LEU cc_start: 0.8647 (tt) cc_final: 0.8204 (mt) REVERT: L 5 LEU cc_start: 0.7468 (pt) cc_final: 0.6790 (mp) REVERT: L 39 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.6921 (tmt-80) REVERT: L 40 ASN cc_start: 0.8134 (t0) cc_final: 0.7888 (t0) REVERT: L 47 VAL cc_start: 0.9088 (t) cc_final: 0.8546 (p) REVERT: P 5 LEU cc_start: 0.8343 (pt) cc_final: 0.8054 (pt) REVERT: Q 5 LEU cc_start: 0.8333 (pt) cc_final: 0.7346 (mp) REVERT: Q 50 MET cc_start: 0.8459 (ptp) cc_final: 0.8100 (ptt) REVERT: Q 67 MET cc_start: 0.7278 (ptm) cc_final: 0.6989 (tmm) REVERT: Q 71 LEU cc_start: 0.6945 (mt) cc_final: 0.6703 (mt) REVERT: Q 72 LEU cc_start: 0.7335 (tp) cc_final: 0.7125 (tp) REVERT: R 3 LEU cc_start: 0.7064 (tt) cc_final: 0.6142 (mt) REVERT: R 44 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7949 (ptmm) REVERT: R 59 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7693 (tt0) REVERT: S 34 ILE cc_start: 0.9488 (mt) cc_final: 0.9177 (tp) REVERT: T 39 ARG cc_start: 0.8992 (ptm160) cc_final: 0.8623 (ptp90) REVERT: 8 29 GLN cc_start: 0.8386 (mp10) cc_final: 0.8062 (mp10) REVERT: 8 34 MET cc_start: 0.7959 (ppp) cc_final: 0.7661 (ppp) REVERT: 8 37 ARG cc_start: 0.8008 (ptm160) cc_final: 0.7604 (ptm160) REVERT: X 31 LEU cc_start: 0.8613 (tt) cc_final: 0.8165 (pp) REVERT: X 72 MET cc_start: 0.9105 (tmm) cc_final: 0.8428 (tmm) REVERT: X 84 LEU cc_start: 0.8662 (mp) cc_final: 0.8040 (tp) REVERT: X 98 ILE cc_start: 0.9057 (mm) cc_final: 0.8835 (mm) REVERT: X 234 TRP cc_start: 0.7900 (t-100) cc_final: 0.7613 (t-100) REVERT: X 236 ILE cc_start: 0.9103 (mm) cc_final: 0.8814 (tp) REVERT: Z 66 THR cc_start: 0.7269 (p) cc_final: 0.6980 (p) REVERT: Z 85 MET cc_start: 0.8491 (mmt) cc_final: 0.8083 (mmt) REVERT: 7 116 ASP cc_start: 0.8067 (t0) cc_final: 0.7836 (m-30) REVERT: U 66 LEU cc_start: 0.8864 (mt) cc_final: 0.8634 (pp) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.1834 time to fit residues: 125.2677 Evaluate side-chains 411 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 106 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 39 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.145129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127945 restraints weight = 23866.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130360 restraints weight = 15907.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.132114 restraints weight = 11668.706| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9599 Z= 0.160 Angle : 0.930 13.809 13029 Z= 0.417 Chirality : 0.047 0.391 1638 Planarity : 0.004 0.049 1561 Dihedral : 21.020 177.418 1704 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1192 helix: 0.01 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -2.47 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP X 126 HIS 0.002 0.001 HIS U 29 PHE 0.044 0.003 PHE K 55 TYR 0.033 0.002 TYR U 82 ARG 0.009 0.001 ARG U 50 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 708) hydrogen bonds : angle 4.41815 ( 2112) covalent geometry : bond 0.00373 ( 9599) covalent geometry : angle 0.93045 (13029) *********************** 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 487 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 0.962 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: K 53 LEU cc_start: 0.7790 (tt) cc_final: 0.7156 (mt) REVERT: L 3 LEU cc_start: 0.8633 (tt) cc_final: 0.8170 (mt) REVERT: L 5 LEU cc_start: 0.7361 (pt) cc_final: 0.6674 (mp) REVERT: L 39 ARG cc_start: 0.7796 (ptm-80) cc_final: 0.6928 (tmt-80) REVERT: L 40 ASN cc_start: 0.8088 (t0) cc_final: 0.7793 (t0) REVERT: L 47 VAL cc_start: 0.8760 (t) cc_final: 0.8361 (p) REVERT: M 43 ILE cc_start: 0.8582 (mt) cc_final: 0.8114 (mm) REVERT: P 5 LEU cc_start: 0.8140 (pt) cc_final: 0.7742 (pt) REVERT: Q 5 LEU cc_start: 0.8201 (pt) cc_final: 0.7236 (mp) REVERT: Q 47 VAL cc_start: 0.8621 (p) cc_final: 0.8201 (p) REVERT: Q 50 MET cc_start: 0.8501 (ptp) cc_final: 0.8119 (ptt) REVERT: R 2 GLN cc_start: 0.6066 (pm20) cc_final: 0.5778 (pm20) REVERT: R 3 LEU cc_start: 0.6894 (tt) cc_final: 0.6189 (mt) REVERT: R 5 LEU cc_start: 0.8156 (pt) cc_final: 0.7011 (pt) REVERT: S 34 ILE cc_start: 0.9465 (mt) cc_final: 0.9177 (tp) REVERT: T 39 ARG cc_start: 0.8952 (ptm160) cc_final: 0.8611 (ptp90) REVERT: T 57 LEU cc_start: 0.7587 (tt) cc_final: 0.7059 (tt) REVERT: 8 34 MET cc_start: 0.8032 (ppp) cc_final: 0.7745 (ppp) REVERT: 8 37 ARG cc_start: 0.8026 (ptm160) cc_final: 0.7541 (ptm160) REVERT: X 31 LEU cc_start: 0.8519 (tt) cc_final: 0.8277 (pp) REVERT: X 44 TYR cc_start: 0.8192 (m-80) cc_final: 0.6395 (m-80) REVERT: X 62 GLN cc_start: 0.8643 (mm-40) cc_final: 0.7954 (mm-40) REVERT: X 72 MET cc_start: 0.9044 (tmm) cc_final: 0.8411 (tmm) REVERT: X 84 LEU cc_start: 0.8546 (mp) cc_final: 0.7919 (tp) REVERT: X 236 ILE cc_start: 0.9034 (mm) cc_final: 0.8766 (tp) REVERT: Z 66 THR cc_start: 0.7251 (p) cc_final: 0.6956 (p) REVERT: 7 116 ASP cc_start: 0.7976 (t0) cc_final: 0.7765 (m-30) REVERT: U 64 LYS cc_start: 0.7645 (ptpt) cc_final: 0.7380 (ptpp) REVERT: U 66 LEU cc_start: 0.8835 (mt) cc_final: 0.8629 (pp) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.1905 time to fit residues: 131.4174 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 : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.0670 chunk 93 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 11 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 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 = 0.4032 r_free = 0.4032 target = 0.144516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127436 restraints weight = 23305.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.129952 restraints weight = 15376.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131487 restraints weight = 11204.537| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.6210 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= 0.174 Angle : 0.959 12.892 13029 Z= 0.430 Chirality : 0.048 0.397 1638 Planarity : 0.004 0.045 1561 Dihedral : 20.332 177.107 1704 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1192 helix: -0.16 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -2.54 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP X 126 HIS 0.003 0.001 HIS X 185 PHE 0.034 0.002 PHE K 55 TYR 0.028 0.002 TYR X 166 ARG 0.009 0.001 ARG U 50 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 708) hydrogen bonds : angle 4.48302 ( 2112) covalent geometry : bond 0.00423 ( 9599) covalent geometry : angle 0.95919 (13029) *********************** 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 476 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 0.943 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 41 PRO cc_start: 0.9108 (Cg_exo) cc_final: 0.8843 (Cg_endo) REVERT: K 45 ASP cc_start: 0.8431 (p0) cc_final: 0.8217 (p0) REVERT: K 53 LEU cc_start: 0.7724 (tt) cc_final: 0.7189 (mt) REVERT: L 3 LEU cc_start: 0.8584 (tt) cc_final: 0.8159 (mt) REVERT: L 5 LEU cc_start: 0.7391 (pt) cc_final: 0.6837 (mp) REVERT: L 39 ARG cc_start: 0.7800 (ptm-80) cc_final: 0.6951 (tmt-80) REVERT: L 40 ASN cc_start: 0.8121 (t0) cc_final: 0.7786 (t0) REVERT: L 47 VAL cc_start: 0.8968 (t) cc_final: 0.8475 (p) REVERT: L 63 LEU cc_start: 0.9098 (mt) cc_final: 0.8840 (mt) REVERT: P 2 GLN cc_start: 0.7586 (tp40) cc_final: 0.6065 (pm20) REVERT: Q 5 LEU cc_start: 0.8172 (pt) cc_final: 0.7261 (mp) REVERT: Q 50 MET cc_start: 0.8464 (ptp) cc_final: 0.8045 (ptt) REVERT: Q 67 MET cc_start: 0.7539 (tmm) cc_final: 0.6994 (ttm) REVERT: R 2 GLN cc_start: 0.6201 (pm20) cc_final: 0.5933 (pm20) REVERT: R 3 LEU cc_start: 0.6988 (tt) cc_final: 0.6220 (mt) REVERT: R 5 LEU cc_start: 0.7968 (pt) cc_final: 0.6787 (pt) REVERT: S 34 ILE cc_start: 0.9455 (mt) cc_final: 0.9169 (tp) REVERT: T 39 ARG cc_start: 0.8976 (ptm160) cc_final: 0.8653 (ptp90) REVERT: 8 34 MET cc_start: 0.8040 (ppp) cc_final: 0.7786 (ppp) REVERT: 8 37 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7387 (ptm160) REVERT: 8 38 LEU cc_start: 0.8846 (tt) cc_final: 0.8588 (tt) REVERT: X 31 LEU cc_start: 0.8683 (tt) cc_final: 0.8340 (pp) REVERT: X 44 TYR cc_start: 0.8158 (m-80) cc_final: 0.6402 (m-80) REVERT: X 62 GLN cc_start: 0.8684 (mm-40) cc_final: 0.7985 (mm-40) REVERT: X 72 MET cc_start: 0.9046 (tmm) cc_final: 0.8393 (tmm) REVERT: X 84 LEU cc_start: 0.8388 (mp) cc_final: 0.7868 (tp) REVERT: X 236 ILE cc_start: 0.9071 (mm) cc_final: 0.8780 (tp) REVERT: Z 66 THR cc_start: 0.7215 (p) cc_final: 0.6989 (p) REVERT: 7 116 ASP cc_start: 0.7990 (t0) cc_final: 0.7775 (m-30) REVERT: 7 128 ARG cc_start: 0.7298 (tpp-160) cc_final: 0.6764 (mmt90) REVERT: U 50 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7844 (mtm-85) REVERT: U 64 LYS cc_start: 0.7697 (ptpt) cc_final: 0.7254 (ptpp) outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 0.1827 time to fit residues: 124.1958 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 : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN X 71 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 169 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 = 0.4036 r_free = 0.4036 target = 0.144718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.127512 restraints weight = 23698.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129899 restraints weight = 15747.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.131605 restraints weight = 11684.938| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9599 Z= 0.174 Angle : 0.976 13.048 13029 Z= 0.441 Chirality : 0.048 0.398 1638 Planarity : 0.004 0.046 1561 Dihedral : 19.937 179.832 1704 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1192 helix: -0.12 (0.16), residues: 1051 sheet: None (None), residues: 0 loop : -2.49 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 14 HIS 0.002 0.001 HIS X 185 PHE 0.057 0.002 PHE K 55 TYR 0.027 0.002 TYR L 9 ARG 0.008 0.001 ARG U 50 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 708) hydrogen bonds : angle 4.51685 ( 2112) covalent geometry : bond 0.00431 ( 9599) covalent geometry : angle 0.97645 (13029) ********************** 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 : 1.059 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: L 3 LEU cc_start: 0.8601 (tt) cc_final: 0.8169 (mt) REVERT: L 5 LEU cc_start: 0.7545 (pt) cc_final: 0.6950 (mp) REVERT: L 39 ARG cc_start: 0.7810 (ptm-80) cc_final: 0.6945 (tmt-80) REVERT: L 40 ASN cc_start: 0.8091 (t0) cc_final: 0.7748 (t0) REVERT: L 47 VAL cc_start: 0.8902 (t) cc_final: 0.8522 (p) REVERT: L 67 MET cc_start: 0.6917 (pmm) cc_final: 0.6074 (mmm) REVERT: O 8 LYS cc_start: 0.7052 (mmtt) cc_final: 0.5032 (mtpt) REVERT: P 2 GLN cc_start: 0.7720 (tp40) cc_final: 0.6078 (pm20) REVERT: P 5 LEU cc_start: 0.8037 (pt) cc_final: 0.7701 (pt) REVERT: P 26 ILE cc_start: 0.9268 (pt) cc_final: 0.8970 (tp) REVERT: Q 5 LEU cc_start: 0.8272 (pt) cc_final: 0.7291 (mp) REVERT: Q 47 VAL cc_start: 0.8636 (p) cc_final: 0.8149 (p) REVERT: Q 50 MET cc_start: 0.8428 (ptp) cc_final: 0.8006 (ptt) REVERT: Q 67 MET cc_start: 0.7461 (tmm) cc_final: 0.7004 (ttm) REVERT: R 2 GLN cc_start: 0.6256 (pm20) cc_final: 0.6018 (pm20) REVERT: R 3 LEU cc_start: 0.6975 (tt) cc_final: 0.6209 (mt) REVERT: R 5 LEU cc_start: 0.8203 (pt) cc_final: 0.7146 (pt) REVERT: S 34 ILE cc_start: 0.9477 (mt) cc_final: 0.9143 (tp) REVERT: T 39 ARG cc_start: 0.8972 (ptm160) cc_final: 0.8676 (ptp90) REVERT: 8 15 TYR cc_start: 0.6202 (m-10) cc_final: 0.5791 (m-80) REVERT: 8 34 MET cc_start: 0.8049 (ppp) cc_final: 0.7754 (ppp) REVERT: 8 37 ARG cc_start: 0.7868 (ptm160) cc_final: 0.7420 (ptm160) REVERT: X 31 LEU cc_start: 0.8652 (tt) cc_final: 0.8364 (pp) REVERT: X 72 MET cc_start: 0.9079 (tmm) cc_final: 0.8430 (tmm) REVERT: X 84 LEU cc_start: 0.8340 (mp) cc_final: 0.7851 (tp) REVERT: X 236 ILE cc_start: 0.9123 (mm) cc_final: 0.8738 (tp) REVERT: 7 128 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.6655 (tpp-160) REVERT: U 64 LYS cc_start: 0.7852 (ptpt) cc_final: 0.7418 (ptpp) REVERT: U 71 LEU cc_start: 0.7220 (tp) cc_final: 0.6561 (pp) REVERT: J 2 LEU cc_start: 0.7591 (mt) cc_final: 0.7195 (mt) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.1778 time to fit residues: 118.5118 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 : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN X 76 GLN U 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.144204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.126918 restraints weight = 23674.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.129314 restraints weight = 15907.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.130976 restraints weight = 11856.506| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6493 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= 0.176 Angle : 0.982 14.612 13029 Z= 0.444 Chirality : 0.048 0.397 1638 Planarity : 0.004 0.044 1561 Dihedral : 19.640 179.227 1704 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1192 helix: -0.06 (0.16), residues: 1049 sheet: None (None), residues: 0 loop : -2.47 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP X 234 HIS 0.003 0.001 HIS X 185 PHE 0.056 0.003 PHE T 70 TYR 0.024 0.002 TYR R 9 ARG 0.014 0.001 ARG U 50 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 708) hydrogen bonds : angle 4.56600 ( 2112) covalent geometry : bond 0.00432 ( 9599) covalent geometry : angle 0.98234 (13029) =============================================================================== Job complete usr+sys time: 4014.15 seconds wall clock time: 74 minutes 2.71 seconds (4442.71 seconds total)