Starting phenix.real_space_refine on Tue Sep 15 08:48:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cp3_7546/09_2026/6cp3_7546.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cp3_7546/09_2026/6cp3_7546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cp3_7546/09_2026/6cp3_7546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cp3_7546/09_2026/6cp3_7546.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6cp3_7546/09_2026/6cp3_7546.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cp3_7546/09_2026/6cp3_7546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cp3_7546/09_2026/6cp3_7546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cp3_7546/09_2026/6cp3_7546.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 92 5.16 5 C 24846 2.51 5 N 6556 2.21 5 O 7375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38882 Number of models: 1 Model: "" Number of chains: 32 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: 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: "Q" 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: "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: "Y" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1317 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3852 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3836 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3865 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3549 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 448} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2086 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1363 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "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: "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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.57, per 1000 atoms: 0.19 Number of scatterers: 38882 At special positions: 0 Unit cell: (127.92, 152.52, 246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 13 15.00 O 7375 8.00 N 6556 7.00 C 24846 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: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9376 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 27 sheets defined 57.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'K' and resid 2 through 15 removed outlier: 4.032A pdb=" N LYS K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR K 9 " --> pdb=" O LEU K 5 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 40 removed outlier: 4.024A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE K 28 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG K 39 " --> pdb=" O ASN K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 74 Proline residue: K 49 - end of helix removed outlier: 3.551A pdb=" N ALA K 56 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N THR K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU K 66 " --> pdb=" O GLY K 62 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 18 through 39 removed outlier: 3.669A pdb=" N ALA L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA L 27 " --> pdb=" O GLY L 23 " (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 72 removed outlier: 3.720A pdb=" N VAL L 47 " --> pdb=" O ILE L 43 " (cutoff:3.500A) Proline residue: L 49 - end of helix removed outlier: 3.667A pdb=" N LEU L 57 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY L 62 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS L 65 " --> pdb=" O THR L 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 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 38 removed outlier: 3.710A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 42 No H-bonds generated for 'chain 'M' and resid 40 through 42' Processing helix chain 'M' and resid 43 through 74 Proline residue: M 49 - end of helix removed outlier: 3.528A pdb=" N ILE M 52 " --> pdb=" O PHE M 48 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 removed outlier: 4.365A pdb=" N ALA N 6 " --> pdb=" O GLN N 2 " (cutoff:3.500A) 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: 4.199A pdb=" N ALA N 27 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER N 38 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 74 Proline residue: N 49 - end of helix removed outlier: 5.170A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 14 removed outlier: 4.102A pdb=" N ALA O 6 " --> pdb=" O GLN O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 18 No H-bonds generated for 'chain 'O' and resid 16 through 18' Processing helix chain 'O' and resid 19 through 38 removed outlier: 4.433A pdb=" N ALA O 27 " --> pdb=" O GLY O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 42 No H-bonds generated for 'chain 'O' and resid 40 through 42' Processing helix chain 'O' and resid 43 through 72 Proline residue: O 49 - end of helix removed outlier: 3.832A pdb=" N LEU O 57 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY O 62 " --> pdb=" O SER O 58 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU O 66 " --> pdb=" O GLY O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 removed outlier: 3.809A pdb=" N ALA P 6 " --> pdb=" O GLN P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 18 No H-bonds generated for 'chain 'P' and resid 16 through 18' Processing helix chain 'P' and resid 19 through 40 removed outlier: 5.174A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE P 28 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG P 39 " --> pdb=" O ASN P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 74 removed outlier: 5.576A pdb=" N THR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY P 62 " --> pdb=" O SER P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 15 Processing helix chain 'Q' and resid 18 through 39 removed outlier: 4.008A pdb=" N ALA Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG Q 39 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 74 removed outlier: 4.415A pdb=" N MET Q 50 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 15 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 39 removed outlier: 3.593A pdb=" N ILE R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 43 through 75 Proline residue: R 49 - end of helix removed outlier: 3.630A pdb=" N LEU R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY R 62 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU R 73 " --> pdb=" O SER R 69 " (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: 4.429A pdb=" N ALA S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL S 29 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG S 39 " --> pdb=" O ASN S 35 " (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: 3.865A pdb=" N ILE S 52 " --> pdb=" O PHE S 48 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY S 54 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS S 65 " --> pdb=" O THR S 61 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.234A 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: 4.532A pdb=" N ALA T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER T 38 " --> pdb=" O ILE T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 removed outlier: 3.663A pdb=" N ALA T 56 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY T 62 " --> pdb=" O SER T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 74 Processing helix chain 'Y' and resid 17 through 29 removed outlier: 3.670A pdb=" N LYS Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 49 Processing helix chain 'Y' and resid 64 through 77 removed outlier: 3.796A pdb=" N THR Y 77 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 96 removed outlier: 4.032A pdb=" N LYS Y 90 " --> pdb=" O VAL Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 117 Processing helix chain 'Y' and resid 130 through 143 removed outlier: 3.802A pdb=" N PHE Y 134 " --> pdb=" O ASP Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 180 through 191 Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.726A pdb=" N LEU A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.530A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 261 removed outlier: 3.542A pdb=" N GLN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.725A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.856A pdb=" N GLU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.673A pdb=" N LYS A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.848A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.908A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.713A pdb=" N GLN A 407 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 413 through 430 removed outlier: 4.423A pdb=" N THR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix removed outlier: 3.801A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 475 removed outlier: 5.432A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.538A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 510 Processing helix chain 'B' and resid 5 through 23 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.663A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.844A pdb=" N ASP B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 4.254A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.523A pdb=" N ASN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.609A pdb=" N LYS B 199 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 262 removed outlier: 3.777A pdb=" N GLN B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.580A pdb=" N ASN B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 285 removed outlier: 3.593A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.712A pdb=" N HIS B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.681A pdb=" N ILE B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.720A pdb=" N PHE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.965A pdb=" N GLN B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.960A pdb=" N PHE B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 430 removed outlier: 3.791A pdb=" N LYS B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix removed outlier: 3.652A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.531A pdb=" N ASP B 456 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 477 removed outlier: 4.108A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 removed outlier: 3.648A pdb=" N LEU B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 removed outlier: 3.689A pdb=" N PHE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 removed outlier: 3.615A pdb=" N GLU C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 removed outlier: 4.057A pdb=" N ASN C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.639A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.812A pdb=" N ASP C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.563A pdb=" N ASN C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 188 through 193' Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 261 removed outlier: 3.666A pdb=" N GLN C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Proline residue: C 249 - end of helix removed outlier: 3.677A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.721A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 4.264A pdb=" N ALA C 295 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.991A pdb=" N SER C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.714A pdb=" N LYS C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 380 removed outlier: 4.034A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 removed outlier: 3.817A pdb=" N VAL C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 403 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.579A pdb=" N GLN C 407 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 removed outlier: 3.578A pdb=" N LYS C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 452 removed outlier: 3.601A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 477 removed outlier: 3.699A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.619A pdb=" N GLN D 127 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 144 removed outlier: 3.659A pdb=" N LEU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 225 through 245 removed outlier: 3.662A pdb=" N ARG D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 270 removed outlier: 3.829A pdb=" N THR D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 325 through 329 removed outlier: 4.006A pdb=" N LEU D 329 " --> pdb=" O PHE D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 385 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 414 removed outlier: 3.558A pdb=" N LEU D 414 " --> pdb=" O ILE D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 447 removed outlier: 3.726A pdb=" N ALA D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 458 removed outlier: 3.514A pdb=" N TYR D 458 " --> pdb=" O HIS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 473 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.507A pdb=" N GLN E 127 " --> pdb=" O PHE E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 162 through 177 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 246 removed outlier: 3.871A pdb=" N ARG E 229 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 Processing helix chain 'E' and resid 284 through 294 removed outlier: 4.557A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 326 Processing helix chain 'E' and resid 336 through 341 removed outlier: 4.208A pdb=" N SER E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 392 removed outlier: 4.619A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 414 Processing helix chain 'E' and resid 433 through 447 removed outlier: 3.978A pdb=" N ALA E 439 " --> pdb=" O LYS E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 458 removed outlier: 3.673A pdb=" N TYR E 458 " --> pdb=" O HIS E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 477 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.560A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 230 removed outlier: 4.099A pdb=" N ARG F 229 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 246 removed outlier: 3.540A pdb=" N PHE F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 269 removed outlier: 4.166A pdb=" N PHE F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 268 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER F 269 " --> pdb=" O GLY F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 313 through 316 removed outlier: 3.556A pdb=" N ASP F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 313 through 316' Processing helix chain 'F' and resid 319 through 326 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 391 removed outlier: 5.093A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 removed outlier: 3.768A pdb=" N GLU F 395 " --> pdb=" O GLY F 392 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU F 396 " --> pdb=" O MET F 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 392 through 396' Processing helix chain 'F' and resid 399 through 414 removed outlier: 3.569A pdb=" N ARG F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.700A pdb=" N THR F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 446 removed outlier: 3.515A pdb=" N THR F 437 " --> pdb=" O ARG F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 478 Processing helix chain 'G' and resid 2 through 55 removed outlier: 3.627A pdb=" N VAL G 6 " --> pdb=" O THR G 2 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 102 removed outlier: 3.976A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.916A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.582A pdb=" N SER G 143 " --> pdb=" O THR G 139 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.710A pdb=" N THR G 158 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 190 removed outlier: 3.548A pdb=" N ILE G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 184 through 190' Processing helix chain 'G' and resid 204 through 272 removed outlier: 4.731A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE G 253 " --> pdb=" O ASN G 249 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP G 269 " --> pdb=" O ASN G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'H' and resid 98 through 113 removed outlier: 3.728A pdb=" N LEU H 104 " --> pdb=" O ASN H 100 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU H 105 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 138 removed outlier: 3.547A pdb=" N GLU H 122 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 24 Processing helix chain 'I' and resid 31 through 38 Processing helix chain 'Z' and resid 55 through 112 removed outlier: 5.253A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.604A pdb=" N ARG Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 133 removed outlier: 4.297A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP Z 125 " --> pdb=" O LYS Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 184 removed outlier: 3.889A pdb=" N LYS Z 143 " --> pdb=" O GLU Z 139 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 206 removed outlier: 4.664A pdb=" N VAL Z 193 " --> pdb=" O PHE Z 189 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN Z 195 " --> pdb=" O GLU Z 191 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER Z 206 " --> pdb=" O GLU Z 202 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 19 Processing helix chain '7' and resid 26 through 48 removed outlier: 3.830A pdb=" N LEU 7 43 " --> pdb=" O ALA 7 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER 7 48 " --> pdb=" O LEU 7 44 " (cutoff:3.500A) Processing helix chain '7' and resid 56 through 61 removed outlier: 3.957A pdb=" N SER 7 60 " --> pdb=" O SER 7 56 " (cutoff:3.500A) Processing helix chain '7' and resid 67 through 78 Processing helix chain '7' and resid 90 through 127 removed outlier: 3.811A pdb=" N SER 7 94 " --> pdb=" O GLN 7 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER 7 126 " --> pdb=" O ASP 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 142 Processing helix chain '7' and resid 142 through 156 removed outlier: 4.340A pdb=" N ASP 7 146 " --> pdb=" O LYS 7 142 " (cutoff:3.500A) Processing helix chain '6' and resid 5 through 17 Processing helix chain '6' and resid 18 through 23 Processing helix chain '6' and resid 46 through 51 Processing helix chain '6' and resid 74 through 92 removed outlier: 4.591A pdb=" N LEU 6 80 " --> pdb=" O GLU 6 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 30 removed outlier: 4.089A pdb=" N LYS U 22 " --> pdb=" O ALA U 18 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 56 Processing helix chain 'U' and resid 63 through 85 removed outlier: 4.138A pdb=" N TYR U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER U 79 " --> pdb=" O ALA U 75 " (cutoff:3.500A) Processing helix chain '8' and resid 8 through 30 Processing helix chain '8' and resid 32 through 48 removed outlier: 3.901A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 27 through 42 Processing helix chain 'X' and resid 56 through 78 removed outlier: 4.052A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) removed outlier: 3.506A 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 100 removed outlier: 3.775A pdb=" N PHE X 95 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 138 Processing helix chain 'X' and resid 139 through 146 removed outlier: 3.510A pdb=" N LEU X 144 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL X 146 " --> pdb=" O SER X 143 " (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 167 removed outlier: 3.601A pdb=" N LEU X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL X 159 " --> pdb=" O VAL X 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE X 167 " --> pdb=" O THR X 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 167 through 197 removed outlier: 4.350A pdb=" N LEU X 173 " --> pdb=" O ARG X 169 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER X 179 " --> pdb=" O LEU X 175 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU X 187 " --> pdb=" O ALA X 183 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA X 192 " --> pdb=" O MET X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 207 removed outlier: 3.515A pdb=" N VAL X 207 " --> pdb=" O PHE X 204 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 247 removed outlier: 3.557A pdb=" N ALA X 225 " --> pdb=" O MET X 221 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 34 removed outlier: 3.990A pdb=" N PHE J 17 " --> pdb=" O TYR J 13 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 122 through 124 Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 37 removed outlier: 5.441A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 65 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.852A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 68 removed outlier: 3.947A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN B 95 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLU B 56 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR B 93 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS F 75 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS F 40 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA F 15 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.479A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB1, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AB2, first strand: chain 'C' and resid 62 through 68 removed outlier: 3.944A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LYS D 75 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS D 40 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 15 " --> pdb=" O ASP D 22 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB4, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.954A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.778A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR C 331 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY C 171 " --> pdb=" O THR C 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.209A pdb=" N ILE D 96 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER D 182 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL D 218 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY D 220 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY D 186 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE D 181 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE D 254 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL D 310 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU D 155 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS D 152 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR D 333 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY D 154 " --> pdb=" O THR D 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 132 through 134 removed outlier: 4.568A pdb=" N GLU D 132 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 134 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 17 removed outlier: 5.253A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AC3, first strand: chain 'E' and resid 133 through 134 removed outlier: 4.501A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 215 through 221 removed outlier: 5.660A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS E 152 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC6, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.967A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 253 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 177 through 183 removed outlier: 3.913A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE G 107 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ILE G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR G 109 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR I 44 " --> pdb=" O THR I 57 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 23 through 27 removed outlier: 5.048A pdb=" N SER H 23 " --> pdb=" O PHE H 14 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE H 14 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS H 11 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL H 85 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 41 removed outlier: 6.982A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) 2073 hydrogen bonds defined for protein. 6021 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: 7.81 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11511 1.33 - 1.46: 7159 1.46 - 1.58: 20652 1.58 - 1.70: 21 1.70 - 1.82: 168 Bond restraints: 39511 Sorted by residual: bond pdb=" CA LYS Y 145 " pdb=" C LYS Y 145 " ideal model delta sigma weight residual 1.524 1.428 0.096 1.26e-02 6.30e+03 5.76e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.31e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.78e+01 ... (remaining 39506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 53116 4.82 - 9.65: 399 9.65 - 14.47: 25 14.47 - 19.30: 2 19.30 - 24.12: 6 Bond angle restraints: 53548 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 115.75 24.12 1.00e+00 1.00e+00 5.82e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 115.94 23.93 1.00e+00 1.00e+00 5.73e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.30 22.57 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 115.23 21.60 1.00e+00 1.00e+00 4.67e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.57 20.26 1.00e+00 1.00e+00 4.10e+02 ... (remaining 53543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 22404 16.26 - 32.52: 1042 32.52 - 48.78: 276 48.78 - 65.04: 32 65.04 - 81.30: 23 Dihedral angle restraints: 23777 sinusoidal: 9173 harmonic: 14604 Sorted by residual: dihedral pdb=" CA ALA E 278 " pdb=" C ALA E 278 " pdb=" N VAL E 279 " pdb=" CA VAL E 279 " ideal model delta harmonic sigma weight residual 180.00 -125.20 -54.80 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA ALA D 278 " pdb=" C ALA D 278 " pdb=" N VAL D 279 " pdb=" CA VAL D 279 " ideal model delta harmonic sigma weight residual 180.00 -132.18 -47.82 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA GLY 6 26 " pdb=" C GLY 6 26 " pdb=" N ASN 6 27 " pdb=" CA ASN 6 27 " ideal model delta harmonic sigma weight residual 180.00 -136.52 -43.48 0 5.00e+00 4.00e-02 7.56e+01 ... (remaining 23774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5733 0.099 - 0.198: 587 0.198 - 0.297: 28 0.297 - 0.396: 2 0.396 - 0.496: 2 Chirality restraints: 6352 Sorted by residual: chirality pdb=" CB ILE U 5 " pdb=" CA ILE U 5 " pdb=" CG1 ILE U 5 " pdb=" CG2 ILE U 5 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CA GLU Y 16 " pdb=" N GLU Y 16 " pdb=" C GLU Y 16 " pdb=" CB GLU Y 16 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB ILE P 43 " pdb=" CA ILE P 43 " pdb=" CG1 ILE P 43 " pdb=" CG2 ILE P 43 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 6349 not shown) Planarity restraints: 6846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO D 322 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA 6 17 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO 6 18 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO 6 18 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO 6 18 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO U 6 " -0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO U 7 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO U 7 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO U 7 " -0.047 5.00e-02 4.00e+02 ... (remaining 6843 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4121 2.74 - 3.28: 39538 3.28 - 3.82: 65869 3.82 - 4.36: 77181 4.36 - 4.90: 127858 Nonbonded interactions: 314567 Sorted by model distance: nonbonded pdb=" O GLY Y 172 " pdb=" OD1 ASP Y 173 " model vdw 2.196 3.040 nonbonded pdb=" O ALA M 12 " pdb=" OG1 THR M 16 " model vdw 2.224 3.040 nonbonded pdb=" O ARG C 130 " pdb=" OG SER C 254 " model vdw 2.242 3.040 nonbonded pdb=" O VAL E 87 " pdb=" OG SER E 111 " model vdw 2.247 3.040 nonbonded pdb=" OG SER C 378 " pdb=" O VAL D 423 " model vdw 2.267 3.040 ... (remaining 314562 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 'A' and (resid 4 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 through 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 45 or (resid 46 and (n \ ame N or name CA or name C or name O or name CB )) or resid 47 through 509 or re \ sid 600)) selection = (chain 'B' and (resid 4 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 600)) selection = (chain 'C' and (resid 4 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 28 or (resid 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 45 or (re \ sid 46 and (name N or name CA or name C or name O or name CB )) or resid 47 thro \ ugh 509 or resid 600)) } ncs_group { reference = (chain 'D' and resid 7 through 475) selection = (chain 'E' and resid 7 through 475) selection = (chain 'F' and resid 7 through 475) } 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 74)) selection = chain 'L' 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 74)) selection = chain 'N' 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 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 74)) selection = chain 'Q' 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 74)) selection = chain 'S' 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 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: 2.810 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: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 32.880 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.009 0.126 39511 Z= 0.417 Angle : 1.182 24.119 53548 Z= 0.673 Chirality : 0.061 0.496 6352 Planarity : 0.008 0.089 6846 Dihedral : 11.105 81.304 14401 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.29 % Favored : 92.41 % Rotamer: Outliers : 1.07 % Allowed : 4.56 % Favored : 94.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.10), residues: 5062 helix: -2.52 (0.08), residues: 2510 sheet: -2.15 (0.19), residues: 584 loop : -2.53 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 229 TYR 0.033 0.003 TYR C 339 PHE 0.023 0.003 PHE X 224 TRP 0.037 0.004 TRP B 258 HIS 0.018 0.003 HIS 6 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.42 (39511) covalent geometry : angle 1.18199 / 0.67 (53548) hydrogen bonds : bond 0.17294 / 11.26 ( 2073) hydrogen bonds : angle 7.94005 / 5.63 ( 6021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 1500 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 63 LEU cc_start: 0.7987 (mt) cc_final: 0.7686 (tt) REVERT: L 5 LEU cc_start: 0.6078 (pt) cc_final: 0.5813 (pt) REVERT: L 63 LEU cc_start: 0.8049 (mt) cc_final: 0.7592 (mt) REVERT: M 48 PHE cc_start: 0.7076 (t80) cc_final: 0.6354 (t80) REVERT: N 15 SER cc_start: 0.6730 (p) cc_final: 0.6524 (t) REVERT: N 50 MET cc_start: 0.7173 (ttm) cc_final: 0.6769 (ttp) REVERT: O 70 PHE cc_start: 0.7400 (m-80) cc_final: 0.7102 (m-80) REVERT: P 41 PRO cc_start: 0.8217 (Cg_exo) cc_final: 0.7837 (Cg_endo) REVERT: P 71 LEU cc_start: 0.7151 (pp) cc_final: 0.6690 (tp) REVERT: P 72 LEU cc_start: 0.6293 (tp) cc_final: 0.5953 (mm) REVERT: Q 55 PHE cc_start: 0.6018 (t80) cc_final: 0.5298 (t80) REVERT: R 46 THR cc_start: 0.7071 (m) cc_final: 0.6664 (m) REVERT: R 47 VAL cc_start: 0.8399 (m) cc_final: 0.8135 (t) REVERT: R 70 PHE cc_start: 0.6577 (t80) cc_final: 0.6330 (t80) REVERT: T 35 ASN cc_start: 0.8299 (m-40) cc_final: 0.7995 (m110) REVERT: Y 138 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 30 THR cc_start: 0.7141 (p) cc_final: 0.6921 (p) REVERT: A 67 ASN cc_start: 0.8151 (m-40) cc_final: 0.7854 (p0) REVERT: A 170 ILE cc_start: 0.9243 (tt) cc_final: 0.9028 (mt) REVERT: A 274 SER cc_start: 0.8341 (m) cc_final: 0.7562 (p) REVERT: A 284 SER cc_start: 0.8389 (m) cc_final: 0.8105 (t) REVERT: A 471 LEU cc_start: 0.8544 (mt) cc_final: 0.7929 (mt) REVERT: B 84 VAL cc_start: 0.8434 (t) cc_final: 0.8223 (t) REVERT: B 138 ILE cc_start: 0.8853 (pt) cc_final: 0.8126 (mt) REVERT: B 153 LYS cc_start: 0.7580 (mtpt) cc_final: 0.7293 (mtpp) REVERT: B 271 ASP cc_start: 0.7381 (t70) cc_final: 0.7075 (t70) REVERT: B 335 ASP cc_start: 0.7756 (t70) cc_final: 0.7549 (p0) REVERT: C 9 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: C 11 SER cc_start: 0.6758 (m) cc_final: 0.4649 (m) REVERT: C 150 THR cc_start: 0.8852 (p) cc_final: 0.8638 (p) REVERT: C 299 ASP cc_start: 0.7740 (p0) cc_final: 0.7520 (p0) REVERT: C 369 VAL cc_start: 0.8230 (t) cc_final: 0.7916 (p) REVERT: D 39 ILE cc_start: 0.9185 (tp) cc_final: 0.8951 (tt) REVERT: D 178 HIS cc_start: 0.5381 (t-90) cc_final: 0.5006 (t70) REVERT: D 222 MET cc_start: 0.7603 (ptp) cc_final: 0.7114 (ptp) REVERT: D 256 ASP cc_start: 0.7930 (t70) cc_final: 0.7726 (t0) REVERT: E 133 ILE cc_start: 0.7518 (mm) cc_final: 0.7217 (mm) REVERT: E 263 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7810 (mm-40) REVERT: F 282 GLN cc_start: 0.8990 (pm20) cc_final: 0.7992 (pm20) REVERT: F 319 ASP cc_start: 0.8233 (t70) cc_final: 0.7824 (t0) REVERT: F 348 VAL cc_start: 0.8878 (t) cc_final: 0.8648 (m) REVERT: F 352 ASP cc_start: 0.6269 (t70) cc_final: 0.5833 (t0) REVERT: F 449 TYR cc_start: 0.7359 (m-80) cc_final: 0.7137 (m-80) REVERT: F 473 LEU cc_start: 0.8179 (mt) cc_final: 0.7955 (mt) REVERT: G 251 TYR cc_start: 0.8405 (m-80) cc_final: 0.8051 (m-80) REVERT: G 255 TYR cc_start: 0.8924 (t80) cc_final: 0.8638 (t80) REVERT: H 51 GLN cc_start: 0.7039 (pt0) cc_final: 0.6510 (pt0) REVERT: Z 133 LEU cc_start: 0.7450 (mt) cc_final: 0.7241 (tt) REVERT: Z 179 ARG cc_start: 0.5753 (mpp80) cc_final: 0.4376 (mmp80) REVERT: 7 43 LEU cc_start: 0.8290 (pp) cc_final: 0.7886 (mt) REVERT: 6 60 THR cc_start: 0.6963 (p) cc_final: 0.6375 (t) REVERT: 6 87 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6693 (mm-30) REVERT: U 48 LEU cc_start: 0.6901 (mp) cc_final: 0.6671 (mp) REVERT: 8 36 LEU cc_start: 0.8574 (tt) cc_final: 0.8331 (tt) REVERT: 8 37 ARG cc_start: 0.7312 (mtp180) cc_final: 0.7043 (tpp80) REVERT: X 51 ASN cc_start: 0.5624 (m-40) cc_final: 0.4953 (m-40) REVERT: X 96 ILE cc_start: 0.8848 (mt) cc_final: 0.8647 (mm) REVERT: X 131 ILE cc_start: 0.7868 (mm) cc_final: 0.7651 (mm) REVERT: X 173 LEU cc_start: 0.7066 (tp) cc_final: 0.6482 (tp) REVERT: X 215 MET cc_start: 0.6417 (ttp) cc_final: 0.5921 (tpt) REVERT: X 232 TYR cc_start: 0.7822 (t80) cc_final: 0.7492 (t80) REVERT: X 237 LEU cc_start: 0.8884 (mp) cc_final: 0.8493 (mt) REVERT: J 4 ARG cc_start: 0.6709 (ttt180) cc_final: 0.6454 (ttm170) outliers start: 44 outliers final: 7 residues processed: 1521 average time/residue: 0.2466 time to fit residues: 597.7416 Evaluate side-chains 824 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 816 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 38 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 2 GLN P 2 GLN Y 188 ASN A 145 HIS A 217 GLN A 220 GLN A 332 GLN A 407 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN B 398 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN C 478 HIS D 27 GLN D 118 HIS D 367 HIS D 385 GLN E 35 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN Z 93 ASN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 88 GLN ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 38 ASN U 29 HIS U 85 HIS 8 29 GLN ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS X 180 ASN X 185 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.109976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087323 restraints weight = 111476.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088017 restraints weight = 69992.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088423 restraints weight = 46441.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088674 restraints weight = 44591.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088879 restraints weight = 39763.375| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39511 Z= 0.197 Angle : 0.789 14.566 53548 Z= 0.394 Chirality : 0.047 0.315 6352 Planarity : 0.005 0.073 6846 Dihedral : 6.895 83.183 5482 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.29 % Favored : 95.52 % Rotamer: Outliers : 3.46 % Allowed : 13.17 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.11), residues: 5062 helix: -0.90 (0.09), residues: 2664 sheet: -1.71 (0.21), residues: 529 loop : -1.94 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 7 128 TYR 0.029 0.002 TYR 7 74 PHE 0.034 0.002 PHE S 64 TRP 0.028 0.002 TRP X 234 HIS 0.013 0.001 HIS 6 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (39511) covalent geometry : angle 0.78938 / 0.39 (53548) hydrogen bonds : bond 0.04769 / 3.21 ( 2073) hydrogen bonds : angle 5.54724 / 3.91 ( 6021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 876 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 71 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7972 (mm) REVERT: L 43 ILE cc_start: 0.8282 (mm) cc_final: 0.7942 (tp) REVERT: L 70 PHE cc_start: 0.8351 (m-80) cc_final: 0.7932 (m-80) REVERT: N 57 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.5926 (mt) REVERT: P 30 PHE cc_start: 0.7617 (m-80) cc_final: 0.7255 (m-80) REVERT: P 41 PRO cc_start: 0.8285 (Cg_exo) cc_final: 0.7865 (Cg_endo) REVERT: P 48 PHE cc_start: 0.7333 (t80) cc_final: 0.7020 (m-80) REVERT: P 57 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6490 (mm) REVERT: P 71 LEU cc_start: 0.7880 (pp) cc_final: 0.7605 (mt) REVERT: Q 34 ILE cc_start: 0.9590 (mt) cc_final: 0.9286 (tt) REVERT: R 55 PHE cc_start: 0.8172 (t80) cc_final: 0.7953 (t80) REVERT: S 5 LEU cc_start: 0.8142 (pt) cc_final: 0.7698 (pt) REVERT: S 9 TYR cc_start: 0.6477 (m-10) cc_final: 0.6002 (m-80) REVERT: T 64 PHE cc_start: 0.7802 (m-80) cc_final: 0.7486 (m-80) REVERT: T 67 MET cc_start: 0.8256 (ppp) cc_final: 0.7854 (ppp) REVERT: Y 138 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 172 ASP cc_start: 0.7310 (t0) cc_final: 0.7054 (t0) REVERT: A 274 SER cc_start: 0.8859 (m) cc_final: 0.8395 (p) REVERT: B 239 SER cc_start: 0.9012 (p) cc_final: 0.8369 (t) REVERT: B 335 ASP cc_start: 0.8356 (t70) cc_final: 0.7594 (t0) REVERT: C 9 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: C 369 VAL cc_start: 0.8729 (t) cc_final: 0.8446 (p) REVERT: D 294 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7535 (mm-30) REVERT: D 334 VAL cc_start: 0.9160 (t) cc_final: 0.8919 (p) REVERT: D 409 LYS cc_start: 0.8774 (mttm) cc_final: 0.8463 (mmtm) REVERT: E 405 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7478 (pt0) REVERT: F 64 MET cc_start: 0.8636 (mmm) cc_final: 0.8302 (mmp) REVERT: F 282 GLN cc_start: 0.9229 (pm20) cc_final: 0.8027 (pm20) REVERT: F 284 THR cc_start: 0.8627 (p) cc_final: 0.8182 (t) REVERT: F 352 ASP cc_start: 0.6603 (t70) cc_final: 0.6384 (t0) REVERT: G 59 ASN cc_start: 0.7824 (p0) cc_final: 0.6018 (t0) REVERT: G 176 GLU cc_start: 0.8228 (tp30) cc_final: 0.7856 (tp30) REVERT: G 237 MET cc_start: 0.7935 (mmp) cc_final: 0.7713 (mmt) REVERT: G 255 TYR cc_start: 0.9244 (t80) cc_final: 0.8902 (t80) REVERT: H 11 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8184 (mmmt) REVERT: H 86 THR cc_start: 0.8827 (m) cc_final: 0.8299 (p) REVERT: Z 82 ASP cc_start: 0.7470 (t0) cc_final: 0.7260 (t0) REVERT: Z 170 ARG cc_start: 0.7822 (tpt90) cc_final: 0.7473 (tmt-80) REVERT: Z 179 ARG cc_start: 0.6378 (mpp80) cc_final: 0.5142 (mmp80) REVERT: 7 28 GLN cc_start: 0.8876 (pm20) cc_final: 0.8578 (pm20) REVERT: 7 170 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7532 (tp) REVERT: 6 60 THR cc_start: 0.7136 (p) cc_final: 0.6657 (t) REVERT: 6 80 LEU cc_start: 0.7758 (tp) cc_final: 0.7450 (mt) REVERT: 6 87 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6476 (mm-30) REVERT: 8 17 PHE cc_start: 0.6387 (t80) cc_final: 0.5985 (t80) REVERT: 8 20 MET cc_start: 0.8162 (tmm) cc_final: 0.7948 (tmm) REVERT: 8 34 MET cc_start: 0.8572 (ppp) cc_final: 0.8203 (ppp) REVERT: 8 48 LEU cc_start: 0.7841 (tp) cc_final: 0.7638 (mt) REVERT: X 38 LEU cc_start: 0.8859 (tp) cc_final: 0.8473 (pp) REVERT: X 63 GLU cc_start: 0.8366 (tp30) cc_final: 0.7551 (tp30) REVERT: X 173 LEU cc_start: 0.8200 (tp) cc_final: 0.7631 (tp) REVERT: X 176 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8395 (ttm110) REVERT: X 181 ILE cc_start: 0.7488 (mm) cc_final: 0.6895 (tt) outliers start: 142 outliers final: 71 residues processed: 957 average time/residue: 0.2180 time to fit residues: 346.3046 Evaluate side-chains 784 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 708 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 141 GLN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 44 LEU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 50 ARG Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 455 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 362 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 409 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 236 optimal weight: 2.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 141 GLN G 217 GLN H 29 GLN H 51 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN Z 93 ASN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS U 85 HIS ** X 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 230 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.110329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087301 restraints weight = 111711.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.087646 restraints weight = 72769.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088046 restraints weight = 52365.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088550 restraints weight = 45495.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088672 restraints weight = 39205.554| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39511 Z= 0.138 Angle : 0.707 12.481 53548 Z= 0.348 Chirality : 0.044 0.186 6352 Planarity : 0.004 0.070 6846 Dihedral : 6.306 80.968 5478 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 3.71 % Allowed : 14.80 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.12), residues: 5062 helix: -0.25 (0.10), residues: 2699 sheet: -1.47 (0.22), residues: 520 loop : -1.70 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 8 42 TYR 0.035 0.002 TYR X 241 PHE 0.032 0.002 PHE H 96 TRP 0.030 0.001 TRP X 234 HIS 0.009 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (39511) covalent geometry : angle 0.70729 / 0.35 (53548) hydrogen bonds : bond 0.04130 / 2.77 ( 2073) hydrogen bonds : angle 5.13838 / 3.62 ( 6021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 822 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7433 (mm) REVERT: L 20 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6446 (mm) REVERT: L 53 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6765 (tt) REVERT: M 46 THR cc_start: 0.7879 (m) cc_final: 0.7478 (m) REVERT: N 39 ARG cc_start: 0.7076 (ptt180) cc_final: 0.6775 (ptt180) REVERT: N 57 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.5560 (mt) REVERT: P 28 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8496 (pt) REVERT: P 30 PHE cc_start: 0.7568 (m-80) cc_final: 0.7093 (m-80) REVERT: P 57 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6357 (mp) REVERT: P 71 LEU cc_start: 0.7920 (pp) cc_final: 0.7679 (tp) REVERT: P 72 LEU cc_start: 0.6768 (tp) cc_final: 0.6217 (mm) REVERT: Q 3 LEU cc_start: 0.4988 (OUTLIER) cc_final: 0.4748 (pp) REVERT: Q 5 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6754 (tp) REVERT: Q 34 ILE cc_start: 0.9589 (mt) cc_final: 0.9293 (tt) REVERT: Q 47 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.7836 (p) REVERT: R 5 LEU cc_start: 0.8552 (tp) cc_final: 0.8281 (tp) REVERT: R 40 ASN cc_start: 0.8410 (t0) cc_final: 0.8196 (t0) REVERT: R 59 GLU cc_start: 0.8021 (pp20) cc_final: 0.7771 (pp20) REVERT: R 73 LEU cc_start: 0.8671 (tp) cc_final: 0.8399 (tt) REVERT: S 5 LEU cc_start: 0.7826 (pt) cc_final: 0.7159 (pt) REVERT: S 9 TYR cc_start: 0.6551 (m-10) cc_final: 0.6046 (m-80) REVERT: A 272 ASP cc_start: 0.8132 (p0) cc_final: 0.7399 (p0) REVERT: A 274 SER cc_start: 0.8794 (m) cc_final: 0.7903 (p) REVERT: B 228 MET cc_start: 0.7659 (mmm) cc_final: 0.7403 (mmm) REVERT: B 239 SER cc_start: 0.8937 (p) cc_final: 0.8212 (t) REVERT: B 335 ASP cc_start: 0.8496 (t70) cc_final: 0.7806 (p0) REVERT: C 9 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: C 150 THR cc_start: 0.9382 (p) cc_final: 0.9164 (p) REVERT: C 369 VAL cc_start: 0.8680 (t) cc_final: 0.8373 (p) REVERT: D 281 TYR cc_start: 0.8670 (m-80) cc_final: 0.8425 (m-10) REVERT: D 294 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7480 (mm-30) REVERT: D 334 VAL cc_start: 0.9196 (t) cc_final: 0.8913 (p) REVERT: D 409 LYS cc_start: 0.8769 (mttm) cc_final: 0.8476 (mmtm) REVERT: E 263 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: E 267 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6888 (mt-10) REVERT: F 64 MET cc_start: 0.8712 (mmm) cc_final: 0.8133 (mmp) REVERT: F 169 GLU cc_start: 0.8184 (tp30) cc_final: 0.7829 (tp30) REVERT: F 222 MET cc_start: 0.7591 (ptp) cc_final: 0.7366 (mtm) REVERT: F 282 GLN cc_start: 0.9240 (pm20) cc_final: 0.8008 (pm20) REVERT: F 284 THR cc_start: 0.8677 (p) cc_final: 0.8321 (t) REVERT: F 352 ASP cc_start: 0.6781 (t70) cc_final: 0.6473 (t0) REVERT: G 59 ASN cc_start: 0.7784 (p0) cc_final: 0.6122 (t0) REVERT: G 237 MET cc_start: 0.8062 (mmp) cc_final: 0.7816 (mmp) REVERT: H 11 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8247 (mmmt) REVERT: H 86 THR cc_start: 0.8795 (m) cc_final: 0.8424 (p) REVERT: H 107 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7878 (pt0) REVERT: H 125 ILE cc_start: 0.9246 (mt) cc_final: 0.8948 (mm) REVERT: I 13 TYR cc_start: 0.8333 (t80) cc_final: 0.8084 (t80) REVERT: I 28 GLU cc_start: 0.6337 (pm20) cc_final: 0.5948 (pm20) REVERT: Z 82 ASP cc_start: 0.7846 (t0) cc_final: 0.7320 (t0) REVERT: Z 179 ARG cc_start: 0.6632 (mpp80) cc_final: 0.5470 (mmp80) REVERT: 7 28 GLN cc_start: 0.8873 (pm20) cc_final: 0.8595 (pm20) REVERT: 7 35 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7667 (mtt180) REVERT: 7 41 ARG cc_start: 0.7574 (ppt170) cc_final: 0.7069 (ppt170) REVERT: 7 100 MET cc_start: 0.8303 (ptm) cc_final: 0.8026 (ptp) REVERT: 6 80 LEU cc_start: 0.7680 (tp) cc_final: 0.7478 (mt) REVERT: 6 87 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6484 (mm-30) REVERT: U 34 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7455 (pp) REVERT: U 64 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7584 (mmtt) REVERT: 8 17 PHE cc_start: 0.6322 (t80) cc_final: 0.5892 (t80) REVERT: 8 20 MET cc_start: 0.8636 (tmm) cc_final: 0.8382 (tmm) REVERT: 8 27 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8629 (t80) REVERT: 8 34 MET cc_start: 0.8431 (ppp) cc_final: 0.8105 (ppp) REVERT: X 32 TYR cc_start: 0.7409 (m-10) cc_final: 0.7040 (m-80) REVERT: X 38 LEU cc_start: 0.8917 (tp) cc_final: 0.8465 (pp) REVERT: X 63 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: X 76 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7342 (tm-30) REVERT: X 85 TYR cc_start: 0.7755 (m-10) cc_final: 0.7505 (m-10) REVERT: X 176 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8490 (ttp-110) REVERT: X 181 ILE cc_start: 0.7444 (mm) cc_final: 0.6956 (tt) REVERT: X 224 PHE cc_start: 0.7393 (m-80) cc_final: 0.6894 (m-80) outliers start: 152 outliers final: 87 residues processed: 906 average time/residue: 0.2166 time to fit residues: 328.9824 Evaluate side-chains 818 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 717 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 76 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain Z residue 93 ASN Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 50 ARG Chi-restraints excluded: chain 8 residue 13 LEU Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 403 optimal weight: 3.9990 chunk 483 optimal weight: 20.0000 chunk 293 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 290 optimal weight: 0.7980 chunk 328 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 446 optimal weight: 9.9990 chunk 407 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 486 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 HIS A 407 GLN B 304 HIS ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 HIS ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN H 51 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 47 GLN ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS 8 29 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082774 restraints weight = 112091.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083369 restraints weight = 70521.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083634 restraints weight = 50238.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084013 restraints weight = 44824.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.084039 restraints weight = 39119.908| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 39511 Z= 0.240 Angle : 0.764 12.221 53548 Z= 0.379 Chirality : 0.046 0.217 6352 Planarity : 0.005 0.072 6846 Dihedral : 6.241 77.856 5476 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.52 % Favored : 95.34 % Rotamer: Outliers : 4.51 % Allowed : 16.12 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 5062 helix: 0.04 (0.10), residues: 2675 sheet: -1.29 (0.22), residues: 527 loop : -1.66 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 7 20 TYR 0.039 0.002 TYR Q 9 PHE 0.031 0.002 PHE E 418 TRP 0.024 0.002 TRP X 234 HIS 0.006 0.002 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (39511) covalent geometry : angle 0.76356 / 0.38 (53548) hydrogen bonds : bond 0.04291 / 2.87 ( 2073) hydrogen bonds : angle 5.14916 / 3.62 ( 6021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 726 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 73 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7424 (mm) REVERT: L 70 PHE cc_start: 0.8188 (m-80) cc_final: 0.7525 (m-80) REVERT: N 24 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8379 (pt) REVERT: N 72 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7662 (tp) REVERT: P 30 PHE cc_start: 0.7432 (m-80) cc_final: 0.7072 (m-80) REVERT: P 57 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6643 (mm) REVERT: Q 34 ILE cc_start: 0.9595 (mt) cc_final: 0.9288 (tt) REVERT: Q 40 ASN cc_start: 0.7984 (t0) cc_final: 0.7635 (t0) REVERT: Q 48 PHE cc_start: 0.8071 (t80) cc_final: 0.7781 (t80) REVERT: Q 59 GLU cc_start: 0.8017 (pt0) cc_final: 0.7805 (pt0) REVERT: R 19 LEU cc_start: 0.7069 (pp) cc_final: 0.6160 (tp) REVERT: R 40 ASN cc_start: 0.8406 (t0) cc_final: 0.8136 (t0) REVERT: R 59 GLU cc_start: 0.8052 (pp20) cc_final: 0.7778 (pp20) REVERT: S 35 ASN cc_start: 0.8993 (m-40) cc_final: 0.8673 (m-40) REVERT: Y 77 THR cc_start: 0.6020 (OUTLIER) cc_final: 0.5816 (m) REVERT: A 172 ASP cc_start: 0.7546 (t0) cc_final: 0.7279 (t0) REVERT: A 272 ASP cc_start: 0.8297 (p0) cc_final: 0.7445 (p0) REVERT: A 274 SER cc_start: 0.9078 (m) cc_final: 0.8238 (p) REVERT: B 89 LEU cc_start: 0.8307 (mm) cc_final: 0.8100 (mt) REVERT: B 335 ASP cc_start: 0.8802 (t70) cc_final: 0.7993 (p0) REVERT: C 369 VAL cc_start: 0.8887 (t) cc_final: 0.8656 (p) REVERT: D 294 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7547 (mm-30) REVERT: D 409 LYS cc_start: 0.8785 (mttm) cc_final: 0.8557 (mmtm) REVERT: E 64 MET cc_start: 0.9048 (mmm) cc_final: 0.8365 (mmt) REVERT: E 153 ILE cc_start: 0.9570 (OUTLIER) cc_final: 0.9294 (mp) REVERT: E 316 ASP cc_start: 0.8059 (t0) cc_final: 0.6954 (m-30) REVERT: F 282 GLN cc_start: 0.9316 (pm20) cc_final: 0.8148 (pm20) REVERT: F 284 THR cc_start: 0.8827 (p) cc_final: 0.8516 (t) REVERT: F 352 ASP cc_start: 0.7084 (t70) cc_final: 0.6792 (t0) REVERT: G 15 ASN cc_start: 0.8429 (t0) cc_final: 0.7977 (t0) REVERT: G 59 ASN cc_start: 0.7729 (p0) cc_final: 0.6065 (t0) REVERT: G 176 GLU cc_start: 0.8246 (tp30) cc_final: 0.7769 (tm-30) REVERT: H 11 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8412 (mmmt) REVERT: H 86 THR cc_start: 0.9010 (m) cc_final: 0.8728 (p) REVERT: H 130 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7817 (tp) REVERT: I 28 GLU cc_start: 0.6374 (pm20) cc_final: 0.6029 (pm20) REVERT: Z 179 ARG cc_start: 0.6621 (mpp80) cc_final: 0.5130 (mmp80) REVERT: 7 28 GLN cc_start: 0.8901 (pm20) cc_final: 0.8582 (pm20) REVERT: 7 157 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6780 (mttt) REVERT: 7 170 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7462 (tp) REVERT: 6 80 LEU cc_start: 0.7748 (tp) cc_final: 0.7534 (mt) REVERT: 6 87 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6506 (mm-30) REVERT: U 56 PHE cc_start: 0.8261 (m-80) cc_final: 0.7489 (t80) REVERT: U 64 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7824 (mmtt) REVERT: U 74 ILE cc_start: 0.8904 (mt) cc_final: 0.8428 (tp) REVERT: U 83 TYR cc_start: 0.6261 (t80) cc_final: 0.5939 (m-10) REVERT: U 84 PHE cc_start: 0.6785 (m-10) cc_final: 0.6538 (m-10) REVERT: 8 17 PHE cc_start: 0.6275 (t80) cc_final: 0.5840 (t80) REVERT: 8 20 MET cc_start: 0.8827 (tmm) cc_final: 0.8539 (tmm) REVERT: 8 27 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8519 (t80) REVERT: 8 34 MET cc_start: 0.8530 (ppp) cc_final: 0.8173 (ppp) REVERT: 8 39 TYR cc_start: 0.7477 (m-10) cc_final: 0.6734 (m-80) REVERT: X 32 TYR cc_start: 0.7463 (m-10) cc_final: 0.7075 (m-80) REVERT: X 63 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: X 76 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7303 (tm-30) REVERT: X 107 TYR cc_start: 0.7457 (m-80) cc_final: 0.7255 (m-80) REVERT: X 176 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8408 (ttp-110) REVERT: X 181 ILE cc_start: 0.7281 (mm) cc_final: 0.6729 (tt) REVERT: X 188 MET cc_start: 0.5374 (OUTLIER) cc_final: 0.4177 (mtp) outliers start: 185 outliers final: 119 residues processed: 846 average time/residue: 0.2156 time to fit residues: 306.7998 Evaluate side-chains 795 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 664 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 157 LYS Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 44 LEU Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 55 TYR Chi-restraints excluded: chain U residue 78 TYR Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 188 MET Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 360 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 370 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 chunk 449 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 498 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 ASN Y 78 HIS A 304 HIS A 432 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 174 GLN C 343 ASN E 57 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS G 217 GLN H 51 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 47 GLN ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS X 62 GLN X 180 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085763 restraints weight = 110643.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086259 restraints weight = 67767.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086821 restraints weight = 46377.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087099 restraints weight = 42975.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087223 restraints weight = 37381.168| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39511 Z= 0.131 Angle : 0.689 13.317 53548 Z= 0.334 Chirality : 0.044 0.257 6352 Planarity : 0.004 0.069 6846 Dihedral : 5.921 77.057 5476 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.37 % Rotamer: Outliers : 3.68 % Allowed : 17.90 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.12), residues: 5062 helix: 0.33 (0.10), residues: 2685 sheet: -1.12 (0.23), residues: 503 loop : -1.44 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 39 TYR 0.025 0.002 TYR X 44 PHE 0.047 0.002 PHE P 64 TRP 0.038 0.002 TRP X 234 HIS 0.010 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (39511) covalent geometry : angle 0.68890 / 0.33 (53548) hydrogen bonds : bond 0.03794 / 2.55 ( 2073) hydrogen bonds : angle 4.87377 / 3.42 ( 6021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 779 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 73 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7442 (mm) REVERT: L 20 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6626 (mm) REVERT: L 53 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6584 (tt) REVERT: M 17 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7624 (mm) REVERT: N 24 ILE cc_start: 0.8618 (mt) cc_final: 0.8315 (pt) REVERT: N 57 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.5402 (mt) REVERT: P 5 LEU cc_start: 0.8147 (pt) cc_final: 0.7660 (tp) REVERT: P 30 PHE cc_start: 0.7464 (m-80) cc_final: 0.7116 (m-80) REVERT: P 46 THR cc_start: 0.6436 (m) cc_final: 0.6233 (m) REVERT: Q 34 ILE cc_start: 0.9584 (mt) cc_final: 0.9291 (tt) REVERT: Q 40 ASN cc_start: 0.7996 (t0) cc_final: 0.7606 (t0) REVERT: Q 59 GLU cc_start: 0.8327 (pt0) cc_final: 0.8126 (pt0) REVERT: R 19 LEU cc_start: 0.7084 (pp) cc_final: 0.6059 (tp) REVERT: S 9 TYR cc_start: 0.6757 (m-10) cc_final: 0.6324 (m-80) REVERT: Y 25 GLN cc_start: 0.8291 (mm110) cc_final: 0.7641 (mm110) REVERT: Y 65 LYS cc_start: 0.8962 (ttpp) cc_final: 0.8713 (tppt) REVERT: Y 94 GLU cc_start: 0.8023 (pt0) cc_final: 0.7785 (pt0) REVERT: A 271 ASP cc_start: 0.8339 (t0) cc_final: 0.8120 (t0) REVERT: A 272 ASP cc_start: 0.8237 (p0) cc_final: 0.7435 (p0) REVERT: A 274 SER cc_start: 0.8947 (m) cc_final: 0.8032 (p) REVERT: B 335 ASP cc_start: 0.8455 (t70) cc_final: 0.7980 (p0) REVERT: C 150 THR cc_start: 0.9405 (p) cc_final: 0.9181 (p) REVERT: C 201 LEU cc_start: 0.9088 (tp) cc_final: 0.8823 (tt) REVERT: C 369 VAL cc_start: 0.8775 (t) cc_final: 0.8513 (p) REVERT: D 294 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7486 (mm-30) REVERT: D 409 LYS cc_start: 0.8699 (mttm) cc_final: 0.8462 (mmtm) REVERT: E 57 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7740 (t0) REVERT: E 64 MET cc_start: 0.9087 (mmm) cc_final: 0.8464 (mmt) REVERT: E 288 ASP cc_start: 0.7399 (m-30) cc_final: 0.7025 (m-30) REVERT: E 316 ASP cc_start: 0.7781 (t0) cc_final: 0.6876 (m-30) REVERT: F 64 MET cc_start: 0.8956 (mmt) cc_final: 0.8717 (mmt) REVERT: F 189 GLU cc_start: 0.6869 (pm20) cc_final: 0.6172 (pm20) REVERT: F 281 TYR cc_start: 0.8768 (m-80) cc_final: 0.8529 (m-80) REVERT: F 282 GLN cc_start: 0.9227 (pm20) cc_final: 0.8051 (pm20) REVERT: F 284 THR cc_start: 0.8782 (p) cc_final: 0.8488 (t) REVERT: F 352 ASP cc_start: 0.7024 (t70) cc_final: 0.6679 (t0) REVERT: F 449 TYR cc_start: 0.7578 (m-80) cc_final: 0.7137 (m-80) REVERT: G 59 ASN cc_start: 0.7563 (p0) cc_final: 0.5967 (t0) REVERT: G 176 GLU cc_start: 0.8144 (tp30) cc_final: 0.7738 (tm-30) REVERT: H 11 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8439 (mmmt) REVERT: H 86 THR cc_start: 0.8927 (m) cc_final: 0.8589 (p) REVERT: H 107 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7939 (mm-30) REVERT: Z 92 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7495 (pp) REVERT: Z 179 ARG cc_start: 0.6399 (mpp80) cc_final: 0.5112 (mmp80) REVERT: 7 28 GLN cc_start: 0.8723 (pm20) cc_final: 0.8515 (pm20) REVERT: 7 47 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (pp30) REVERT: 7 157 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6780 (mttt) REVERT: 6 87 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6199 (mm-30) REVERT: U 56 PHE cc_start: 0.8015 (m-80) cc_final: 0.7249 (t80) REVERT: U 74 ILE cc_start: 0.8908 (mt) cc_final: 0.8464 (tp) REVERT: U 83 TYR cc_start: 0.6095 (t80) cc_final: 0.5800 (m-10) REVERT: U 85 HIS cc_start: 0.5723 (OUTLIER) cc_final: 0.4646 (m-70) REVERT: 8 17 PHE cc_start: 0.6118 (t80) cc_final: 0.5623 (t80) REVERT: 8 27 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8475 (t80) REVERT: 8 34 MET cc_start: 0.8573 (ppp) cc_final: 0.8273 (ppp) REVERT: 8 39 TYR cc_start: 0.7065 (m-10) cc_final: 0.6477 (m-80) REVERT: X 32 TYR cc_start: 0.7484 (m-10) cc_final: 0.7141 (m-80) REVERT: X 63 GLU cc_start: 0.8490 (tp30) cc_final: 0.7797 (tp30) REVERT: X 76 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7532 (tm-30) REVERT: X 176 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8354 (ttp-110) REVERT: X 181 ILE cc_start: 0.7387 (mm) cc_final: 0.6905 (tt) REVERT: X 188 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.4426 (mtp) REVERT: J 27 MET cc_start: 0.7375 (tpt) cc_final: 0.7091 (tpt) outliers start: 151 outliers final: 90 residues processed: 870 average time/residue: 0.2104 time to fit residues: 308.3277 Evaluate side-chains 797 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 695 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 196 GLN Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 47 GLN Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 157 LYS Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 78 TYR Chi-restraints excluded: chain U residue 85 HIS Chi-restraints excluded: chain 8 residue 13 LEU Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 188 MET Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 349 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 382 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 378 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 321 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 489 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 282 GLN B 343 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS D 385 GLN E 57 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN H 51 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.109127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085316 restraints weight = 111662.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085761 restraints weight = 73068.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086059 restraints weight = 49555.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086396 restraints weight = 46770.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086558 restraints weight = 43257.157| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39511 Z= 0.141 Angle : 0.701 13.836 53548 Z= 0.340 Chirality : 0.044 0.360 6352 Planarity : 0.004 0.072 6846 Dihedral : 5.795 76.267 5475 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.77 % Favored : 96.09 % Rotamer: Outliers : 3.98 % Allowed : 18.56 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 5062 helix: 0.51 (0.10), residues: 2687 sheet: -0.97 (0.23), residues: 512 loop : -1.38 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 39 TYR 0.024 0.002 TYR D 381 PHE 0.048 0.002 PHE P 64 TRP 0.035 0.001 TRP X 234 HIS 0.008 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (39511) covalent geometry : angle 0.70142 / 0.34 (53548) hydrogen bonds : bond 0.03753 / 2.53 ( 2073) hydrogen bonds : angle 4.80368 / 3.38 ( 6021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 722 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7427 (mt) REVERT: L 20 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6573 (mm) REVERT: L 53 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6557 (tt) REVERT: L 70 PHE cc_start: 0.7996 (m-80) cc_final: 0.7338 (m-80) REVERT: M 17 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7643 (mm) REVERT: N 24 ILE cc_start: 0.8684 (mt) cc_final: 0.8370 (pt) REVERT: N 57 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6591 (pt) REVERT: O 59 GLU cc_start: 0.6331 (pt0) cc_final: 0.5809 (tp30) REVERT: P 5 LEU cc_start: 0.8226 (pt) cc_final: 0.7758 (tp) REVERT: P 30 PHE cc_start: 0.7484 (m-80) cc_final: 0.7212 (m-80) REVERT: P 46 THR cc_start: 0.6564 (m) cc_final: 0.6359 (m) REVERT: Q 34 ILE cc_start: 0.9585 (mt) cc_final: 0.9286 (tt) REVERT: Q 40 ASN cc_start: 0.8023 (t0) cc_final: 0.7485 (t0) REVERT: Q 59 GLU cc_start: 0.8362 (pt0) cc_final: 0.8034 (pt0) REVERT: R 19 LEU cc_start: 0.7173 (pp) cc_final: 0.6238 (tp) REVERT: R 40 ASN cc_start: 0.8281 (t0) cc_final: 0.7947 (t0) REVERT: R 43 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8201 (tp) REVERT: R 59 GLU cc_start: 0.8160 (pp20) cc_final: 0.7929 (pp20) REVERT: Y 185 GLN cc_start: 0.8798 (tp40) cc_final: 0.8314 (tm-30) REVERT: A 153 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: A 271 ASP cc_start: 0.8213 (t0) cc_final: 0.7870 (t0) REVERT: A 272 ASP cc_start: 0.8427 (p0) cc_final: 0.7617 (p0) REVERT: A 274 SER cc_start: 0.8965 (m) cc_final: 0.8003 (p) REVERT: B 335 ASP cc_start: 0.8466 (t70) cc_final: 0.8005 (p0) REVERT: C 9 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: C 150 THR cc_start: 0.9395 (p) cc_final: 0.9164 (p) REVERT: C 201 LEU cc_start: 0.9090 (tp) cc_final: 0.8833 (tt) REVERT: C 369 VAL cc_start: 0.8804 (t) cc_final: 0.8542 (p) REVERT: D 294 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7667 (mm-30) REVERT: E 64 MET cc_start: 0.9144 (mmm) cc_final: 0.8556 (mmt) REVERT: E 316 ASP cc_start: 0.7758 (t0) cc_final: 0.6823 (m-30) REVERT: E 457 PHE cc_start: 0.5877 (OUTLIER) cc_final: 0.5414 (m-80) REVERT: F 64 MET cc_start: 0.8956 (mmt) cc_final: 0.8630 (mmt) REVERT: F 189 GLU cc_start: 0.7191 (pm20) cc_final: 0.6368 (pm20) REVERT: F 282 GLN cc_start: 0.9239 (pm20) cc_final: 0.8056 (pm20) REVERT: F 284 THR cc_start: 0.8788 (p) cc_final: 0.8482 (t) REVERT: F 352 ASP cc_start: 0.7049 (t70) cc_final: 0.6710 (t0) REVERT: G 59 ASN cc_start: 0.7576 (p0) cc_final: 0.6010 (t0) REVERT: G 176 GLU cc_start: 0.8194 (tp30) cc_final: 0.7722 (tm-30) REVERT: H 11 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8367 (mmmt) REVERT: H 86 THR cc_start: 0.8823 (m) cc_final: 0.8494 (p) REVERT: Z 133 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7255 (tt) REVERT: Z 179 ARG cc_start: 0.6422 (mpp80) cc_final: 0.5073 (mmp80) REVERT: 7 28 GLN cc_start: 0.8687 (pm20) cc_final: 0.8424 (pm20) REVERT: 7 35 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7699 (mtt180) REVERT: 6 87 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6268 (mm-30) REVERT: U 56 PHE cc_start: 0.8019 (m-80) cc_final: 0.7238 (t80) REVERT: U 83 TYR cc_start: 0.6087 (t80) cc_final: 0.5750 (m-10) REVERT: 8 17 PHE cc_start: 0.6053 (t80) cc_final: 0.5774 (t80) REVERT: 8 27 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8469 (t80) REVERT: 8 39 TYR cc_start: 0.7325 (m-10) cc_final: 0.6332 (m-80) REVERT: X 32 TYR cc_start: 0.7518 (m-10) cc_final: 0.7161 (m-80) REVERT: X 63 GLU cc_start: 0.8549 (tp30) cc_final: 0.7903 (tp30) REVERT: X 181 ILE cc_start: 0.7481 (mm) cc_final: 0.6998 (tt) REVERT: X 220 MET cc_start: 0.7729 (mmm) cc_final: 0.7154 (mmm) outliers start: 163 outliers final: 112 residues processed: 818 average time/residue: 0.2040 time to fit residues: 283.0909 Evaluate side-chains 799 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 676 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 PHE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 457 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 78 TYR Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 190 ILE Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 303 optimal weight: 9.9990 chunk 443 optimal weight: 20.0000 chunk 413 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 372 optimal weight: 1.9990 chunk 402 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 2 GLN ** P 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS B 343 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS E 118 HIS ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 88 GLN ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 12 GLN X 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.108070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083770 restraints weight = 111755.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085215 restraints weight = 65316.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085388 restraints weight = 45088.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085866 restraints weight = 40772.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085952 restraints weight = 35884.258| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39511 Z= 0.168 Angle : 0.717 14.647 53548 Z= 0.349 Chirality : 0.045 0.318 6352 Planarity : 0.004 0.071 6846 Dihedral : 5.768 78.413 5475 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 4.05 % Allowed : 19.07 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 5062 helix: 0.59 (0.10), residues: 2683 sheet: -0.99 (0.22), residues: 531 loop : -1.29 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 39 TYR 0.031 0.002 TYR 6 7 PHE 0.047 0.002 PHE P 64 TRP 0.031 0.002 TRP X 234 HIS 0.008 0.001 HIS U 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (39511) covalent geometry : angle 0.71735 / 0.35 (53548) hydrogen bonds : bond 0.03808 / 2.56 ( 2073) hydrogen bonds : angle 4.80085 / 3.37 ( 6021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 712 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7773 (mm) REVERT: L 53 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6544 (tt) REVERT: L 70 PHE cc_start: 0.8105 (m-80) cc_final: 0.7400 (m-80) REVERT: M 17 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7558 (mm) REVERT: M 74 PHE cc_start: 0.6047 (m-80) cc_final: 0.5687 (m-80) REVERT: P 5 LEU cc_start: 0.8338 (pt) cc_final: 0.7890 (tp) REVERT: P 30 PHE cc_start: 0.7552 (m-80) cc_final: 0.7304 (m-80) REVERT: P 46 THR cc_start: 0.6742 (m) cc_final: 0.6474 (m) REVERT: Q 34 ILE cc_start: 0.9590 (mt) cc_final: 0.9309 (tt) REVERT: Q 40 ASN cc_start: 0.8196 (t0) cc_final: 0.7618 (t0) REVERT: Q 59 GLU cc_start: 0.8406 (pt0) cc_final: 0.8068 (pt0) REVERT: R 19 LEU cc_start: 0.7287 (pp) cc_final: 0.6516 (tp) REVERT: R 40 ASN cc_start: 0.8373 (t0) cc_final: 0.8060 (t0) REVERT: R 43 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8214 (tp) REVERT: R 59 GLU cc_start: 0.8052 (pp20) cc_final: 0.7799 (pp20) REVERT: Y 185 GLN cc_start: 0.8839 (tp40) cc_final: 0.8349 (tm-30) REVERT: A 272 ASP cc_start: 0.8479 (p0) cc_final: 0.7702 (p0) REVERT: A 274 SER cc_start: 0.9047 (m) cc_final: 0.8129 (p) REVERT: B 213 SER cc_start: 0.9359 (p) cc_final: 0.8965 (t) REVERT: B 335 ASP cc_start: 0.8534 (t70) cc_final: 0.8136 (p0) REVERT: C 9 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: C 150 THR cc_start: 0.9392 (p) cc_final: 0.9161 (p) REVERT: C 201 LEU cc_start: 0.9121 (tp) cc_final: 0.8875 (tt) REVERT: D 169 GLU cc_start: 0.7086 (tp30) cc_final: 0.6827 (mm-30) REVERT: D 294 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7693 (mm-30) REVERT: E 64 MET cc_start: 0.9170 (mmm) cc_final: 0.8605 (mmt) REVERT: E 153 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9137 (mp) REVERT: E 263 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: E 267 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7420 (mt-10) REVERT: E 457 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.5560 (m-80) REVERT: F 189 GLU cc_start: 0.7235 (pm20) cc_final: 0.6336 (pm20) REVERT: F 282 GLN cc_start: 0.9272 (pm20) cc_final: 0.7983 (pm20) REVERT: F 284 THR cc_start: 0.8860 (p) cc_final: 0.8575 (t) REVERT: F 352 ASP cc_start: 0.7073 (t70) cc_final: 0.6756 (t0) REVERT: F 449 TYR cc_start: 0.7612 (m-80) cc_final: 0.7140 (m-80) REVERT: G 59 ASN cc_start: 0.7479 (p0) cc_final: 0.6003 (t0) REVERT: G 176 GLU cc_start: 0.8191 (tp30) cc_final: 0.7785 (tm-30) REVERT: H 11 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8330 (mmmt) REVERT: H 86 THR cc_start: 0.8934 (m) cc_final: 0.8587 (p) REVERT: Z 133 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7348 (tt) REVERT: 7 28 GLN cc_start: 0.8611 (pm20) cc_final: 0.8349 (pm20) REVERT: 6 80 LEU cc_start: 0.7600 (tp) cc_final: 0.7382 (mt) REVERT: 6 87 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6472 (mm-30) REVERT: U 56 PHE cc_start: 0.8014 (m-80) cc_final: 0.7272 (t80) REVERT: 8 17 PHE cc_start: 0.6134 (t80) cc_final: 0.5835 (t80) REVERT: X 32 TYR cc_start: 0.7610 (m-10) cc_final: 0.7338 (m-80) REVERT: X 169 ARG cc_start: 0.8803 (ttm170) cc_final: 0.8457 (mtp85) REVERT: X 176 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8406 (ttp-110) REVERT: X 181 ILE cc_start: 0.7575 (mm) cc_final: 0.7129 (tt) REVERT: J 27 MET cc_start: 0.7611 (tpt) cc_final: 0.7272 (tpt) outliers start: 166 outliers final: 125 residues processed: 807 average time/residue: 0.2141 time to fit residues: 292.8808 Evaluate side-chains 795 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 661 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 PHE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 457 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 341 GLU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 44 LEU Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 55 TYR Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 78 TYR Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 190 ILE Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 159 optimal weight: 0.8980 chunk 459 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 201 optimal weight: 20.0000 chunk 313 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 498 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 305 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** 7 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 57 ASN ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084219 restraints weight = 111621.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084562 restraints weight = 71634.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084812 restraints weight = 48982.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085126 restraints weight = 46906.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085294 restraints weight = 43866.562| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 39511 Z= 0.173 Angle : 0.724 13.164 53548 Z= 0.353 Chirality : 0.045 0.295 6352 Planarity : 0.004 0.072 6846 Dihedral : 5.768 78.196 5475 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.05 % Rotamer: Outliers : 4.02 % Allowed : 19.56 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.12), residues: 5062 helix: 0.66 (0.10), residues: 2687 sheet: -1.01 (0.22), residues: 551 loop : -1.25 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 39 TYR 0.040 0.002 TYR 7 74 PHE 0.047 0.002 PHE P 64 TRP 0.031 0.002 TRP X 234 HIS 0.007 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (39511) covalent geometry : angle 0.72432 / 0.35 (53548) hydrogen bonds : bond 0.03796 / 2.54 ( 2073) hydrogen bonds : angle 4.81507 / 3.39 ( 6021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 693 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7679 (mm) REVERT: L 70 PHE cc_start: 0.8080 (m-80) cc_final: 0.7357 (m-80) REVERT: M 17 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7646 (mm) REVERT: M 74 PHE cc_start: 0.5776 (m-80) cc_final: 0.5483 (m-80) REVERT: O 59 GLU cc_start: 0.6634 (pt0) cc_final: 0.5928 (tp30) REVERT: P 5 LEU cc_start: 0.8288 (pt) cc_final: 0.7866 (tp) REVERT: P 30 PHE cc_start: 0.7405 (m-80) cc_final: 0.7195 (m-80) REVERT: Q 34 ILE cc_start: 0.9609 (mt) cc_final: 0.9344 (tt) REVERT: Q 40 ASN cc_start: 0.8286 (t0) cc_final: 0.7740 (t0) REVERT: Q 59 GLU cc_start: 0.8347 (pt0) cc_final: 0.8007 (pt0) REVERT: R 19 LEU cc_start: 0.7244 (pp) cc_final: 0.6723 (tp) REVERT: R 30 PHE cc_start: 0.8241 (m-80) cc_final: 0.7913 (m-80) REVERT: R 34 ILE cc_start: 0.9272 (tp) cc_final: 0.9003 (pt) REVERT: R 40 ASN cc_start: 0.8317 (t0) cc_final: 0.8087 (t0) REVERT: R 59 GLU cc_start: 0.8026 (pp20) cc_final: 0.7817 (pp20) REVERT: Y 65 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8638 (tppt) REVERT: Y 113 ASP cc_start: 0.8120 (p0) cc_final: 0.7847 (p0) REVERT: Y 185 GLN cc_start: 0.8831 (tp40) cc_final: 0.8357 (tm-30) REVERT: A 27 LEU cc_start: 0.7943 (mt) cc_final: 0.7730 (mt) REVERT: A 272 ASP cc_start: 0.8436 (p0) cc_final: 0.7651 (p0) REVERT: A 274 SER cc_start: 0.9089 (m) cc_final: 0.8185 (p) REVERT: B 213 SER cc_start: 0.9407 (p) cc_final: 0.9061 (t) REVERT: B 330 GLU cc_start: 0.7460 (tp30) cc_final: 0.7083 (tp30) REVERT: C 9 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: C 150 THR cc_start: 0.9388 (p) cc_final: 0.9142 (p) REVERT: C 201 LEU cc_start: 0.9129 (tp) cc_final: 0.8888 (tt) REVERT: D 169 GLU cc_start: 0.7072 (tp30) cc_final: 0.6860 (mm-30) REVERT: D 222 MET cc_start: 0.7946 (ptp) cc_final: 0.7656 (mtm) REVERT: D 294 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7746 (mm-30) REVERT: E 64 MET cc_start: 0.9186 (mmm) cc_final: 0.8634 (mmt) REVERT: E 153 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9160 (mp) REVERT: E 263 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: E 267 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7452 (mt-10) REVERT: E 316 ASP cc_start: 0.7804 (t0) cc_final: 0.6880 (m-30) REVERT: E 457 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5613 (m-80) REVERT: E 458 TYR cc_start: 0.7438 (t80) cc_final: 0.7076 (t80) REVERT: F 189 GLU cc_start: 0.7137 (pm20) cc_final: 0.6371 (pm20) REVERT: F 242 TYR cc_start: 0.8006 (t80) cc_final: 0.7749 (t80) REVERT: F 282 GLN cc_start: 0.9253 (pm20) cc_final: 0.8567 (pm20) REVERT: F 284 THR cc_start: 0.8852 (p) cc_final: 0.8643 (t) REVERT: F 352 ASP cc_start: 0.7427 (t70) cc_final: 0.7056 (t0) REVERT: F 449 TYR cc_start: 0.7667 (m-80) cc_final: 0.7152 (m-80) REVERT: G 59 ASN cc_start: 0.7561 (p0) cc_final: 0.6024 (t0) REVERT: G 176 GLU cc_start: 0.8272 (tp30) cc_final: 0.7914 (tm-30) REVERT: H 11 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8338 (mmmt) REVERT: H 86 THR cc_start: 0.8893 (m) cc_final: 0.8645 (p) REVERT: Z 133 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7402 (tt) REVERT: 7 28 GLN cc_start: 0.8585 (pm20) cc_final: 0.8329 (pm20) REVERT: 6 9 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7419 (tpm170) REVERT: 6 80 LEU cc_start: 0.7660 (tp) cc_final: 0.7446 (mt) REVERT: 6 87 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6471 (mm-30) REVERT: U 56 PHE cc_start: 0.7825 (m-80) cc_final: 0.7095 (t80) REVERT: X 63 GLU cc_start: 0.8568 (tp30) cc_final: 0.7811 (tp30) REVERT: X 176 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8250 (ttp-110) REVERT: X 181 ILE cc_start: 0.7431 (mm) cc_final: 0.7037 (tt) REVERT: J 27 MET cc_start: 0.7488 (tpt) cc_final: 0.7204 (tpt) outliers start: 165 outliers final: 125 residues processed: 791 average time/residue: 0.2127 time to fit residues: 285.7496 Evaluate side-chains 790 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 658 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 70 PHE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 457 PHE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 341 GLU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 167 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 44 LEU Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 55 TYR Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 78 TYR Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 190 ILE Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 239 optimal weight: 1.9990 chunk 440 optimal weight: 10.0000 chunk 374 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 2 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN B 343 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 ASN ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 4 GLN ** 6 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.109116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085348 restraints weight = 111938.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085880 restraints weight = 71729.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086442 restraints weight = 49291.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086826 restraints weight = 43200.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086873 restraints weight = 38708.046| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39511 Z= 0.138 Angle : 0.723 13.261 53548 Z= 0.349 Chirality : 0.045 0.413 6352 Planarity : 0.004 0.071 6846 Dihedral : 5.695 78.541 5475 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.69 % Favored : 96.17 % Rotamer: Outliers : 3.41 % Allowed : 20.66 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.12), residues: 5062 helix: 0.78 (0.10), residues: 2682 sheet: -0.88 (0.22), residues: 547 loop : -1.12 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 8 42 TYR 0.025 0.001 TYR U 51 PHE 0.048 0.002 PHE P 64 TRP 0.032 0.002 TRP X 234 HIS 0.008 0.001 HIS U 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (39511) covalent geometry : angle 0.72284 / 0.35 (53548) hydrogen bonds : bond 0.03669 / 2.45 ( 2073) hydrogen bonds : angle 4.75252 / 3.34 ( 6021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 707 time to evaluate : 1.424 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 73 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7810 (mm) REVERT: L 70 PHE cc_start: 0.8028 (m-80) cc_final: 0.7243 (m-80) REVERT: M 17 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7733 (mm) REVERT: M 67 MET cc_start: 0.6067 (tpt) cc_final: 0.5549 (tpp) REVERT: M 74 PHE cc_start: 0.5812 (m-80) cc_final: 0.5538 (m-80) REVERT: O 48 PHE cc_start: 0.7775 (t80) cc_final: 0.7366 (t80) REVERT: O 59 GLU cc_start: 0.6473 (pt0) cc_final: 0.5867 (tp30) REVERT: P 5 LEU cc_start: 0.8243 (pt) cc_final: 0.7867 (tp) REVERT: P 30 PHE cc_start: 0.7565 (m-80) cc_final: 0.7329 (m-80) REVERT: P 48 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: P 67 MET cc_start: 0.7602 (pp-130) cc_final: 0.5876 (mpp) REVERT: Q 34 ILE cc_start: 0.9588 (mt) cc_final: 0.9311 (tt) REVERT: Q 40 ASN cc_start: 0.8313 (t0) cc_final: 0.7755 (t0) REVERT: Q 59 GLU cc_start: 0.8394 (pt0) cc_final: 0.8064 (pt0) REVERT: R 30 PHE cc_start: 0.8272 (m-80) cc_final: 0.7906 (m-80) REVERT: R 34 ILE cc_start: 0.9247 (tp) cc_final: 0.8947 (pt) REVERT: R 59 GLU cc_start: 0.8061 (pp20) cc_final: 0.7778 (pp20) REVERT: S 9 TYR cc_start: 0.7199 (m-10) cc_final: 0.6929 (m-80) REVERT: S 63 LEU cc_start: 0.8562 (mm) cc_final: 0.8344 (mm) REVERT: S 64 PHE cc_start: 0.8305 (m-80) cc_final: 0.8103 (m-10) REVERT: Y 11 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8458 (mmm160) REVERT: Y 65 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8641 (tppt) REVERT: Y 113 ASP cc_start: 0.8085 (p0) cc_final: 0.7790 (p0) REVERT: Y 185 GLN cc_start: 0.8844 (tp40) cc_final: 0.8326 (tm-30) REVERT: A 27 LEU cc_start: 0.7808 (mt) cc_final: 0.7594 (mt) REVERT: A 272 ASP cc_start: 0.8411 (p0) cc_final: 0.7628 (p0) REVERT: A 274 SER cc_start: 0.9048 (m) cc_final: 0.8105 (p) REVERT: A 340 ILE cc_start: 0.9550 (mm) cc_final: 0.9320 (mt) REVERT: B 213 SER cc_start: 0.9390 (p) cc_final: 0.9013 (t) REVERT: B 330 GLU cc_start: 0.7427 (tp30) cc_final: 0.7042 (tp30) REVERT: B 335 ASP cc_start: 0.8511 (t70) cc_final: 0.8160 (p0) REVERT: C 9 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: C 150 THR cc_start: 0.9395 (p) cc_final: 0.9160 (p) REVERT: C 201 LEU cc_start: 0.9144 (tp) cc_final: 0.8906 (tt) REVERT: D 294 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7668 (mm-30) REVERT: D 381 TYR cc_start: 0.7843 (t80) cc_final: 0.7334 (t80) REVERT: E 64 MET cc_start: 0.9187 (mmm) cc_final: 0.8624 (mmt) REVERT: E 169 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6288 (mm-30) REVERT: E 263 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8018 (tp-100) REVERT: E 267 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7634 (mt-10) REVERT: E 316 ASP cc_start: 0.7591 (t0) cc_final: 0.6775 (m-30) REVERT: E 457 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: E 458 TYR cc_start: 0.7511 (t80) cc_final: 0.7108 (t80) REVERT: F 64 MET cc_start: 0.8754 (mmt) cc_final: 0.7847 (mmp) REVERT: F 189 GLU cc_start: 0.7065 (pm20) cc_final: 0.6305 (pm20) REVERT: F 242 TYR cc_start: 0.7953 (t80) cc_final: 0.7716 (t80) REVERT: F 282 GLN cc_start: 0.9218 (pm20) cc_final: 0.7940 (pm20) REVERT: F 284 THR cc_start: 0.8791 (p) cc_final: 0.8548 (t) REVERT: F 352 ASP cc_start: 0.7409 (t70) cc_final: 0.7050 (t0) REVERT: G 59 ASN cc_start: 0.7485 (p0) cc_final: 0.6065 (t0) REVERT: G 176 GLU cc_start: 0.8188 (tp30) cc_final: 0.7898 (tm-30) REVERT: G 211 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: H 11 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8339 (mmmt) REVERT: H 86 THR cc_start: 0.8817 (m) cc_final: 0.8553 (p) REVERT: H 107 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7981 (mm-30) REVERT: Z 133 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7358 (tt) REVERT: Z 170 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7555 (mmm160) REVERT: Z 179 ARG cc_start: 0.6357 (mpp80) cc_final: 0.5168 (mmp80) REVERT: 7 28 GLN cc_start: 0.8565 (pm20) cc_final: 0.8343 (pm20) REVERT: 6 9 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7332 (tpm170) REVERT: 6 80 LEU cc_start: 0.7588 (tp) cc_final: 0.7385 (mt) REVERT: 6 87 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6521 (mm-30) REVERT: U 56 PHE cc_start: 0.7827 (m-80) cc_final: 0.7096 (t80) REVERT: 8 20 MET cc_start: 0.8329 (ppp) cc_final: 0.8069 (ppp) REVERT: X 63 GLU cc_start: 0.8556 (tp30) cc_final: 0.7817 (tp30) REVERT: X 169 ARG cc_start: 0.8729 (ttm170) cc_final: 0.8407 (mtp85) REVERT: X 181 ILE cc_start: 0.7524 (mm) cc_final: 0.7146 (tt) REVERT: X 220 MET cc_start: 0.7545 (mmm) cc_final: 0.6576 (ttp) REVERT: J 27 MET cc_start: 0.7529 (tpt) cc_final: 0.7262 (tpt) outliers start: 140 outliers final: 115 residues processed: 789 average time/residue: 0.2091 time to fit residues: 280.2437 Evaluate side-chains 797 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 675 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 48 PHE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 70 PHE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 457 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 78 TYR Chi-restraints excluded: chain U residue 83 TYR Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 190 ILE Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 168 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 315 optimal weight: 6.9990 chunk 419 optimal weight: 2.9990 chunk 211 optimal weight: 0.0570 chunk 130 optimal weight: 5.9990 chunk 323 optimal weight: 0.7980 chunk 382 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 413 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 35 ASN ** P 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 4 GLN 6 92 HIS U 14 ASN ** X 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085600 restraints weight = 111111.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086166 restraints weight = 71118.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086521 restraints weight = 52119.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087047 restraints weight = 44442.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087108 restraints weight = 38590.010| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 39511 Z= 0.139 Angle : 0.723 12.771 53548 Z= 0.351 Chirality : 0.045 0.406 6352 Planarity : 0.004 0.071 6846 Dihedral : 5.639 79.205 5475 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 3.10 % Allowed : 21.27 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 5062 helix: 0.81 (0.10), residues: 2692 sheet: -0.81 (0.22), residues: 535 loop : -1.03 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 8 42 TYR 0.039 0.002 TYR X 32 PHE 0.047 0.002 PHE P 64 TRP 0.028 0.002 TRP X 234 HIS 0.008 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (39511) covalent geometry : angle 0.72282 / 0.35 (53548) hydrogen bonds : bond 0.03674 / 2.47 ( 2073) hydrogen bonds : angle 4.71121 / 3.31 ( 6021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10124 Ramachandran restraints generated. 5062 Oldfield, 0 Emsley, 5062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 712 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 PHE cc_start: 0.8012 (m-80) cc_final: 0.7222 (m-80) REVERT: M 17 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7692 (mm) REVERT: M 67 MET cc_start: 0.6043 (tpt) cc_final: 0.5539 (tpp) REVERT: M 74 PHE cc_start: 0.5663 (m-80) cc_final: 0.5440 (m-80) REVERT: N 72 LEU cc_start: 0.7928 (tp) cc_final: 0.7555 (tp) REVERT: O 48 PHE cc_start: 0.7811 (t80) cc_final: 0.7482 (t80) REVERT: O 59 GLU cc_start: 0.6640 (pt0) cc_final: 0.6033 (tp30) REVERT: P 5 LEU cc_start: 0.8212 (pt) cc_final: 0.7823 (tp) REVERT: P 30 PHE cc_start: 0.7596 (m-80) cc_final: 0.7378 (m-80) REVERT: Q 34 ILE cc_start: 0.9582 (mt) cc_final: 0.9342 (tt) REVERT: Q 40 ASN cc_start: 0.8373 (t0) cc_final: 0.7787 (t0) REVERT: Q 50 MET cc_start: 0.7449 (ptp) cc_final: 0.7143 (ptp) REVERT: Q 59 GLU cc_start: 0.8398 (pt0) cc_final: 0.8052 (pt0) REVERT: R 19 LEU cc_start: 0.7219 (pp) cc_final: 0.6684 (tp) REVERT: R 30 PHE cc_start: 0.8272 (m-80) cc_final: 0.7883 (m-80) REVERT: R 34 ILE cc_start: 0.9218 (tp) cc_final: 0.8917 (pt) REVERT: Y 65 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8661 (tppt) REVERT: Y 113 ASP cc_start: 0.8111 (p0) cc_final: 0.7802 (p0) REVERT: Y 185 GLN cc_start: 0.8843 (tp40) cc_final: 0.8299 (tm-30) REVERT: A 27 LEU cc_start: 0.7688 (mt) cc_final: 0.7483 (mt) REVERT: A 272 ASP cc_start: 0.8395 (p0) cc_final: 0.7575 (p0) REVERT: A 274 SER cc_start: 0.9057 (m) cc_final: 0.8103 (p) REVERT: A 340 ILE cc_start: 0.9583 (mm) cc_final: 0.9351 (mt) REVERT: B 213 SER cc_start: 0.9385 (p) cc_final: 0.9019 (t) REVERT: B 335 ASP cc_start: 0.8547 (t70) cc_final: 0.8131 (p0) REVERT: C 9 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: C 150 THR cc_start: 0.9374 (p) cc_final: 0.9138 (p) REVERT: C 201 LEU cc_start: 0.9128 (tp) cc_final: 0.8896 (tt) REVERT: D 294 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 381 TYR cc_start: 0.7749 (t80) cc_final: 0.7193 (t80) REVERT: E 64 MET cc_start: 0.9201 (mmm) cc_final: 0.8657 (mmt) REVERT: E 169 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6150 (mm-30) REVERT: E 263 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8052 (tp-100) REVERT: E 316 ASP cc_start: 0.7551 (t0) cc_final: 0.6762 (m-30) REVERT: F 242 TYR cc_start: 0.7944 (t80) cc_final: 0.7714 (t80) REVERT: F 282 GLN cc_start: 0.9218 (pm20) cc_final: 0.7933 (pm20) REVERT: F 352 ASP cc_start: 0.7233 (t70) cc_final: 0.6910 (t0) REVERT: F 390 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8720 (mt) REVERT: G 59 ASN cc_start: 0.7313 (p0) cc_final: 0.5895 (t0) REVERT: G 176 GLU cc_start: 0.8163 (tp30) cc_final: 0.7886 (tm-30) REVERT: H 11 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8350 (mmmt) REVERT: H 14 PHE cc_start: 0.8325 (t80) cc_final: 0.7856 (t80) REVERT: H 107 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7935 (mm-30) REVERT: Z 82 ASP cc_start: 0.6539 (p0) cc_final: 0.6281 (p0) REVERT: Z 86 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8908 (ptpp) REVERT: Z 133 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7387 (tt) REVERT: Z 170 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7559 (mmm160) REVERT: 7 28 GLN cc_start: 0.8565 (pm20) cc_final: 0.8348 (pm20) REVERT: 6 9 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7255 (tpm170) REVERT: 6 87 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6231 (mm-30) REVERT: 8 20 MET cc_start: 0.8311 (ppp) cc_final: 0.8077 (ppp) REVERT: X 63 GLU cc_start: 0.8559 (tp30) cc_final: 0.7782 (tp30) REVERT: X 176 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8308 (ttp-110) REVERT: X 181 ILE cc_start: 0.7565 (mm) cc_final: 0.7164 (tt) REVERT: X 199 MET cc_start: 0.3748 (mmp) cc_final: 0.2073 (mpp) REVERT: X 220 MET cc_start: 0.7384 (mmm) cc_final: 0.7077 (mmm) REVERT: J 27 MET cc_start: 0.7503 (tpt) cc_final: 0.7247 (tpt) outliers start: 127 outliers final: 102 residues processed: 783 average time/residue: 0.2121 time to fit residues: 283.0449 Evaluate side-chains 783 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 676 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 55 PHE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 9 TYR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 70 PHE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain Y residue 86 VAL Chi-restraints excluded: chain Y residue 152 SER Chi-restraints excluded: chain Y residue 178 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 341 GLU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain Z residue 115 ASN Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 42 GLN Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 92 HIS Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 78 TYR Chi-restraints excluded: chain 8 residue 24 LEU Chi-restraints excluded: chain 8 residue 35 ILE Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 190 ILE Chi-restraints excluded: chain X residue 207 VAL Chi-restraints excluded: chain X residue 211 VAL Chi-restraints excluded: chain J residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 383 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 425 optimal weight: 0.0000 chunk 394 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 483 optimal weight: 9.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 35 ASN ** P 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN A 407 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN B 343 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 4 GLN 6 92 HIS ** X 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.110222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086783 restraints weight = 111418.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086909 restraints weight = 72742.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087671 restraints weight = 48911.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087920 restraints weight = 43713.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088090 restraints weight = 38821.997| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 39511 Z= 0.130 Angle : 0.737 13.023 53548 Z= 0.354 Chirality : 0.045 0.386 6352 Planarity : 0.004 0.075 6846 Dihedral : 5.551 79.494 5473 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.75 % Favored : 96.11 % Rotamer: Outliers : 2.83 % Allowed : 21.63 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 5062 helix: 0.86 (0.10), residues: 2693 sheet: -0.73 (0.22), residues: 535 loop : -0.95 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 8 42 TYR 0.040 0.001 TYR X 32 PHE 0.061 0.002 PHE O 70 TRP 0.025 0.002 TRP X 234 HIS 0.024 0.001 HIS 6 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (39511) covalent geometry : angle 0.73719 / 0.35 (53548) hydrogen bonds : bond 0.03596 / 2.41 ( 2073) hydrogen bonds : angle 4.67800 / 3.28 ( 6021) =============================================================================== Job complete usr+sys time: 7308.65 seconds wall clock time: 127 minutes 2.95 seconds (7622.95 seconds total)