Starting phenix.real_space_refine on Thu Mar 14 18:10:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp5_7547/03_2024/6cp5_7547_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 6335 2.51 5 N 1422 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O GLU 59": "OE1" <-> "OE2" Residue "P PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9413 Number of models: 1 Model: "" Number of chains: 19 Chain: "K" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 364 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "X" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1772 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "Z" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 386 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 52} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "7" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 520 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 63} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 522 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 63} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "N" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 112 Unusual residues: {'EFO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'EFO': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'EFO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.55 Number of scatterers: 9413 At special positions: 0 Unit cell: (84.87, 115.62, 114.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1605 8.00 N 1422 7.00 C 6335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 0 sheets defined 81.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'K' and resid 3 through 37 removed outlier: 3.898A pdb=" N THR K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE K 17 " --> pdb=" O GLY K 13 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU K 19 " --> pdb=" O SER K 15 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 73 removed outlier: 5.020A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 3.646A pdb=" N PHE K 55 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU K 57 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA K 60 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR K 61 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE K 64 " --> pdb=" O THR K 61 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU K 71 " --> pdb=" O VAL K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 38 removed outlier: 4.082A pdb=" N ILE L 17 " --> pdb=" O GLY L 13 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLY L 18 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY L 21 " --> pdb=" O ILE L 17 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA L 27 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 73 removed outlier: 4.776A pdb=" N ASP L 45 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE L 48 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Proline residue: L 49 - end of helix removed outlier: 5.067A pdb=" N LEU L 57 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA L 60 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 39 removed outlier: 3.503A pdb=" N THR M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE M 17 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY M 18 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 73 removed outlier: 4.408A pdb=" N LYS M 44 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP M 45 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE M 48 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Proline residue: M 49 - end of helix removed outlier: 4.982A pdb=" N LEU M 57 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA M 60 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 14 Processing helix chain 'N' and resid 17 through 37 removed outlier: 5.501A pdb=" N ILE N 26 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL N 37 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 73 Proline residue: N 49 - end of helix removed outlier: 4.745A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 15 Processing helix chain 'O' and resid 17 through 37 removed outlier: 4.130A pdb=" N GLY O 21 " --> pdb=" O GLY O 18 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE O 26 " --> pdb=" O GLY O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 73 Proline residue: O 49 - end of helix removed outlier: 3.702A pdb=" N LEU O 57 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY O 62 " --> pdb=" O SER O 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 37 removed outlier: 3.882A pdb=" N ILE P 14 " --> pdb=" O ILE P 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR P 16 " --> pdb=" O ALA P 12 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE P 17 " --> pdb=" O GLY P 13 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLY P 18 " --> pdb=" O ILE P 14 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU P 19 " --> pdb=" O SER P 15 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU P 20 " --> pdb=" O THR P 16 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLY P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 58 Processing helix chain 'P' and resid 63 through 73 removed outlier: 4.234A pdb=" N VAL P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER P 69 " --> pdb=" O CYS P 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 16 removed outlier: 3.824A pdb=" N THR Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 38 removed outlier: 4.953A pdb=" N ALA Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL Q 37 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 73 removed outlier: 4.487A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS Q 65 " --> pdb=" O THR Q 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Q 66 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL Q 68 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 14 Processing helix chain 'R' and resid 17 through 39 removed outlier: 4.631A pdb=" N ILE R 26 " --> pdb=" O GLY R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 71 removed outlier: 4.189A pdb=" N LYS R 44 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP R 45 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Proline residue: R 49 - end of helix removed outlier: 6.064A pdb=" N LEU R 57 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA R 60 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR R 61 " --> pdb=" O SER R 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 38 removed outlier: 4.387A pdb=" N ILE S 17 " --> pdb=" O GLY S 13 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY S 18 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA S 22 " --> pdb=" O GLY S 18 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE S 28 " --> pdb=" O ILE S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 73 removed outlier: 3.910A pdb=" N LYS S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP S 45 " --> pdb=" O SER S 42 " (cutoff:3.500A) Proline residue: S 49 - end of helix removed outlier: 4.087A pdb=" N LEU S 53 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU S 59 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA S 60 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU S 71 " --> pdb=" O VAL S 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 37 removed outlier: 4.059A pdb=" N ILE T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY T 18 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU T 19 " --> pdb=" O SER T 15 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU T 20 " --> pdb=" O THR T 16 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLY T 21 " --> pdb=" O ILE T 17 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 61 removed outlier: 6.267A pdb=" N ASP T 45 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE T 48 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Proline residue: T 49 - end of helix removed outlier: 3.990A pdb=" N ILE T 52 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA T 60 " --> pdb=" O LEU T 57 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR T 61 " --> pdb=" O SER T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 73 Processing helix chain '8' and resid 9 through 47 removed outlier: 5.437A pdb=" N LEU 8 32 " --> pdb=" O SER 8 28 " (cutoff:3.500A) Proline residue: 8 33 - end of helix removed outlier: 3.736A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 44 removed outlier: 3.726A pdb=" N TYR X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 77 removed outlier: 3.743A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE X 77 " --> pdb=" O THR X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 102 Proline residue: X 87 - end of helix removed outlier: 4.349A pdb=" N LEU X 92 " --> pdb=" O ILE X 89 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET X 94 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE X 95 " --> pdb=" O LEU X 92 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA X 99 " --> pdb=" O ILE X 96 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASN X 100 " --> pdb=" O PHE X 97 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE X 102 " --> pdb=" O ALA X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 145 removed outlier: 8.166A pdb=" N TRP X 139 " --> pdb=" O TYR X 135 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL X 140 " --> pdb=" O LYS X 136 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE X 141 " --> pdb=" O HIS X 137 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE X 142 " --> pdb=" O GLY X 138 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER X 143 " --> pdb=" O TRP X 139 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU X 144 " --> pdb=" O VAL X 140 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE X 145 " --> pdb=" O PHE X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 197 Proline residue: X 156 - end of helix removed outlier: 4.090A pdb=" N ILE X 161 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR X 166 " --> pdb=" O THR X 163 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG X 169 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE X 171 " --> pdb=" O ALA X 168 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER X 172 " --> pdb=" O ARG X 169 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY X 174 " --> pdb=" O ILE X 171 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG X 176 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY X 178 " --> pdb=" O LEU X 175 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU X 182 " --> pdb=" O SER X 179 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS X 185 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU X 186 " --> pdb=" O ALA X 183 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU X 191 " --> pdb=" O MET X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 206 Processing helix chain 'X' and resid 211 through 246 removed outlier: 4.223A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 105 removed outlier: 4.820A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.563A pdb=" N ARG Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) Processing helix chain '7' and resid 108 through 124 removed outlier: 3.766A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 141 Processing helix chain '7' and resid 143 through 155 Processing helix chain 'U' and resid 20 through 29 removed outlier: 4.047A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 55 Processing helix chain 'U' and resid 63 through 84 removed outlier: 5.006A pdb=" N GLY U 77 " --> pdb=" O ILE U 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 671 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1447 1.33 - 1.45: 2458 1.45 - 1.57: 5602 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 9599 Sorted by residual: bond pdb=" C18 EFO N 101 " pdb=" C19 EFO N 101 " ideal model delta sigma weight residual 1.922 1.334 0.588 2.00e-02 2.50e+03 8.65e+02 bond pdb=" C18 EFO N 102 " pdb=" C19 EFO N 102 " ideal model delta sigma weight residual 1.922 1.334 0.588 2.00e-02 2.50e+03 8.64e+02 bond pdb=" C18 EFO P 101 " pdb=" C19 EFO P 101 " ideal model delta sigma weight residual 1.922 1.334 0.588 2.00e-02 2.50e+03 8.64e+02 bond pdb=" C18 EFO O 101 " pdb=" C19 EFO O 101 " ideal model delta sigma weight residual 1.922 1.334 0.588 2.00e-02 2.50e+03 8.64e+02 bond pdb=" C7 EFO P 101 " pdb=" C8 EFO P 101 " ideal model delta sigma weight residual 1.075 1.535 -0.460 2.00e-02 2.50e+03 5.29e+02 ... (remaining 9594 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.20: 203 106.20 - 113.15: 5414 113.15 - 120.09: 3411 120.09 - 127.03: 3945 127.03 - 133.97: 56 Bond angle restraints: 13029 Sorted by residual: angle pdb=" C17 EFO O 101 " pdb=" C18 EFO O 101 " pdb=" C19 EFO O 101 " ideal model delta sigma weight residual 86.15 126.89 -40.74 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C17 EFO P 101 " pdb=" C18 EFO P 101 " pdb=" C19 EFO P 101 " ideal model delta sigma weight residual 86.15 126.81 -40.66 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C17 EFO N 101 " pdb=" C18 EFO N 101 " pdb=" C19 EFO N 101 " ideal model delta sigma weight residual 86.15 126.80 -40.65 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C17 EFO N 102 " pdb=" C18 EFO N 102 " pdb=" C19 EFO N 102 " ideal model delta sigma weight residual 86.15 126.79 -40.64 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C18 EFO N 102 " pdb=" C19 EFO N 102 " pdb=" C20 EFO N 102 " ideal model delta sigma weight residual 86.22 125.91 -39.69 3.00e+00 1.11e-01 1.75e+02 ... (remaining 13024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 5414 35.82 - 71.63: 66 71.63 - 107.45: 10 107.45 - 143.27: 30 143.27 - 179.09: 16 Dihedral angle restraints: 5536 sinusoidal: 2057 harmonic: 3479 Sorted by residual: dihedral pdb=" CA PHE 8 30 " pdb=" C PHE 8 30 " pdb=" N PHE 8 31 " pdb=" CA PHE 8 31 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" C15 EFO N 101 " pdb=" C16 EFO N 101 " pdb=" C17 EFO N 101 " pdb=" C18 EFO N 101 " ideal model delta sinusoidal sigma weight residual 72.30 -108.61 -179.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C15 EFO N 102 " pdb=" C16 EFO N 102 " pdb=" C17 EFO N 102 " pdb=" C18 EFO N 102 " ideal model delta sinusoidal sigma weight residual 72.30 -108.63 -179.07 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.078: 1630 1.078 - 2.157: 4 2.157 - 3.235: 0 3.235 - 4.314: 0 4.314 - 5.392: 4 Chirality restraints: 1638 Sorted by residual: chirality pdb=" C25 EFO O 101 " pdb=" C24 EFO O 101 " pdb=" C26 EFO O 101 " pdb=" C2B EFO O 101 " both_signs ideal model delta sigma weight residual False 2.77 -2.62 5.39 2.00e-01 2.50e+01 7.27e+02 chirality pdb=" C25 EFO P 101 " pdb=" C24 EFO P 101 " pdb=" C26 EFO P 101 " pdb=" C2B EFO P 101 " both_signs ideal model delta sigma weight residual False 2.77 -2.62 5.39 2.00e-01 2.50e+01 7.26e+02 chirality pdb=" C25 EFO N 102 " pdb=" C24 EFO N 102 " pdb=" C26 EFO N 102 " pdb=" C2B EFO N 102 " both_signs ideal model delta sigma weight residual False 2.77 -2.62 5.39 2.00e-01 2.50e+01 7.26e+02 ... (remaining 1635 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 EFO O 101 " 0.162 2.00e-02 2.50e+03 2.48e-01 6.16e+02 pdb=" C20 EFO O 101 " -0.383 2.00e-02 2.50e+03 pdb=" C21 EFO O 101 " 0.268 2.00e-02 2.50e+03 pdb=" C22 EFO O 101 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 EFO O 101 " -0.197 2.00e-02 2.50e+03 2.46e-01 6.05e+02 pdb=" C18 EFO O 101 " 0.138 2.00e-02 2.50e+03 pdb=" C19 EFO O 101 " 0.332 2.00e-02 2.50e+03 pdb=" C20 EFO O 101 " -0.272 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C33 EFO P 101 " 0.246 2.00e-02 2.50e+03 2.33e-01 5.44e+02 pdb=" C34 EFO P 101 " -0.330 2.00e-02 2.50e+03 pdb=" C35 EFO P 101 " -0.108 2.00e-02 2.50e+03 pdb=" C36 EFO P 101 " 0.192 2.00e-02 2.50e+03 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 41 2.41 - 3.03: 6320 3.03 - 3.65: 15170 3.65 - 4.28: 21853 4.28 - 4.90: 34255 Nonbonded interactions: 77639 Sorted by model distance: nonbonded pdb=" O LEU Q 63 " pdb=" N CYS Q 65 " model vdw 1.785 2.520 nonbonded pdb=" O SER Q 58 " pdb=" OG1 THR Q 61 " model vdw 1.809 2.440 nonbonded pdb=" O ILE X 160 " pdb=" OG1 THR X 163 " model vdw 1.901 2.440 nonbonded pdb=" CD1 LEU O 57 " pdb=" CZ PHE P 55 " model vdw 1.948 3.760 nonbonded pdb=" CD1 LEU O 57 " pdb=" CE2 PHE P 55 " model vdw 2.004 3.760 ... (remaining 77634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'L' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'M' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'N' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 65 or (resid 66 and (name N or name C \ A or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'Q' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 74)) selection = (chain 'R' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'S' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 74)) selection = (chain 'T' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 60 or (resid 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 74)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.140 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 28.570 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.030 0.588 9599 Z= 1.912 Angle : 1.711 40.736 13029 Z= 0.682 Chirality : 0.281 5.392 1638 Planarity : 0.015 0.248 1561 Dihedral : 20.700 179.085 3310 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.21 % Favored : 92.03 % Rotamer: Outliers : 2.24 % Allowed : 8.64 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.20), residues: 1192 helix: -2.56 (0.13), residues: 973 sheet: None (None), residues: 0 loop : -3.21 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 67 HIS 0.003 0.001 HIS U 68 PHE 0.020 0.001 PHE O 70 TYR 0.014 0.001 TYR J 25 ARG 0.001 0.000 ARG X 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 613 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 43 ILE cc_start: 0.8845 (tp) cc_final: 0.8623 (tp) REVERT: K 67 MET cc_start: 0.8852 (ttp) cc_final: 0.8573 (ttm) REVERT: L 5 LEU cc_start: 0.7455 (pt) cc_final: 0.6755 (mp) REVERT: L 39 ARG cc_start: 0.7325 (ptm-80) cc_final: 0.6999 (tpt170) REVERT: L 47 VAL cc_start: 0.9000 (t) cc_final: 0.8773 (p) REVERT: L 67 MET cc_start: 0.7773 (pp-130) cc_final: 0.7317 (tpt) REVERT: L 68 VAL cc_start: 0.7931 (t) cc_final: 0.7692 (t) REVERT: M 44 LYS cc_start: 0.8549 (ttmt) cc_final: 0.7909 (tptp) REVERT: M 52 ILE cc_start: 0.8649 (tt) cc_final: 0.8437 (tt) REVERT: M 67 MET cc_start: 0.8672 (pp-130) cc_final: 0.8310 (ppp) REVERT: P 5 LEU cc_start: 0.8229 (pt) cc_final: 0.7616 (tp) REVERT: Q 26 ILE cc_start: 0.8297 (pt) cc_final: 0.7883 (pt) REVERT: Q 38 SER cc_start: 0.8386 (p) cc_final: 0.7921 (m) REVERT: R 3 LEU cc_start: 0.6898 (tm) cc_final: 0.6045 (mt) REVERT: R 5 LEU cc_start: 0.8290 (pt) cc_final: 0.7105 (pt) REVERT: R 26 ILE cc_start: 0.8506 (pt) cc_final: 0.7836 (mt) REVERT: S 43 ILE cc_start: 0.8345 (tt) cc_final: 0.8129 (tp) REVERT: 8 26 LEU cc_start: 0.8733 (tt) cc_final: 0.8311 (tt) REVERT: X 31 LEU cc_start: 0.8573 (tt) cc_final: 0.8183 (pp) REVERT: X 56 SER cc_start: 0.7112 (m) cc_final: 0.6817 (m) REVERT: X 81 ASN cc_start: 0.8410 (p0) cc_final: 0.8186 (p0) REVERT: X 84 LEU cc_start: 0.8476 (mp) cc_final: 0.8147 (tp) REVERT: X 92 LEU cc_start: 0.8662 (mt) cc_final: 0.8037 (mt) REVERT: X 98 ILE cc_start: 0.8619 (mm) cc_final: 0.8394 (mm) REVERT: X 120 SER cc_start: 0.8715 (t) cc_final: 0.8507 (p) REVERT: X 164 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6456 (pp) REVERT: X 190 ILE cc_start: 0.7885 (mt) cc_final: 0.7526 (mm) REVERT: 7 128 ARG cc_start: 0.6699 (ttm170) cc_final: 0.6446 (ttm-80) REVERT: 7 148 LYS cc_start: 0.7935 (tttp) cc_final: 0.6732 (ttmt) REVERT: U 32 LYS cc_start: 0.5617 (ttmt) cc_final: 0.5359 (ttpt) REVERT: U 68 HIS cc_start: 0.7759 (m-70) cc_final: 0.7341 (t-170) REVERT: J 1 MET cc_start: 0.6384 (ttp) cc_final: 0.5484 (mtt) outliers start: 21 outliers final: 12 residues processed: 625 average time/residue: 0.1934 time to fit residues: 169.1304 Evaluate side-chains 450 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 437 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 ASN X 185 HIS ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 HIS U 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9599 Z= 0.228 Angle : 1.239 29.583 13029 Z= 0.483 Chirality : 0.109 2.034 1638 Planarity : 0.005 0.047 1561 Dihedral : 26.268 177.568 1404 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 0.32 % Allowed : 5.12 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.22), residues: 1192 helix: -1.55 (0.15), residues: 980 sheet: None (None), residues: 0 loop : -2.74 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP X 126 HIS 0.004 0.001 HIS U 68 PHE 0.049 0.002 PHE O 64 TYR 0.021 0.002 TYR R 9 ARG 0.014 0.001 ARG 8 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 518 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7620 (tt) cc_final: 0.7166 (mt) REVERT: K 67 MET cc_start: 0.8855 (ttp) cc_final: 0.8634 (ttm) REVERT: L 5 LEU cc_start: 0.7370 (pt) cc_final: 0.7036 (mp) REVERT: L 39 ARG cc_start: 0.7490 (ptm-80) cc_final: 0.7117 (tpt170) REVERT: L 40 ASN cc_start: 0.7828 (t0) cc_final: 0.7565 (t0) REVERT: L 47 VAL cc_start: 0.8751 (t) cc_final: 0.8385 (p) REVERT: L 50 MET cc_start: 0.8022 (ppp) cc_final: 0.7550 (ppp) REVERT: M 28 ILE cc_start: 0.8084 (pt) cc_final: 0.6992 (mt) REVERT: M 44 LYS cc_start: 0.8463 (ttmt) cc_final: 0.7821 (tptt) REVERT: O 14 ILE cc_start: 0.8330 (pt) cc_final: 0.8070 (pt) REVERT: O 67 MET cc_start: 0.7680 (ptt) cc_final: 0.7415 (ptt) REVERT: P 2 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7603 (tp40) REVERT: P 5 LEU cc_start: 0.8286 (pt) cc_final: 0.7443 (pt) REVERT: P 44 LYS cc_start: 0.7997 (tptt) cc_final: 0.7646 (tptt) REVERT: Q 5 LEU cc_start: 0.8386 (pt) cc_final: 0.7240 (mp) REVERT: Q 30 PHE cc_start: 0.8018 (m-80) cc_final: 0.7743 (m-80) REVERT: Q 48 PHE cc_start: 0.8051 (t80) cc_final: 0.7629 (t80) REVERT: Q 50 MET cc_start: 0.8734 (ptp) cc_final: 0.8501 (ptt) REVERT: Q 52 ILE cc_start: 0.8091 (tt) cc_final: 0.7768 (mm) REVERT: R 3 LEU cc_start: 0.6893 (tt) cc_final: 0.6207 (mt) REVERT: R 5 LEU cc_start: 0.8203 (pt) cc_final: 0.7125 (pt) REVERT: R 43 ILE cc_start: 0.9101 (tt) cc_final: 0.8833 (tt) REVERT: R 64 PHE cc_start: 0.8272 (m-10) cc_final: 0.7898 (m-10) REVERT: S 43 ILE cc_start: 0.8421 (tt) cc_final: 0.8174 (tp) REVERT: S 57 LEU cc_start: 0.8749 (mt) cc_final: 0.8398 (mt) REVERT: T 46 THR cc_start: 0.7784 (m) cc_final: 0.7524 (m) REVERT: 8 10 MET cc_start: 0.6569 (mmp) cc_final: 0.5277 (mpp) REVERT: 8 34 MET cc_start: 0.8177 (ppp) cc_final: 0.7866 (ppp) REVERT: 8 37 ARG cc_start: 0.7928 (ptm160) cc_final: 0.7643 (ptm160) REVERT: X 31 LEU cc_start: 0.8647 (tt) cc_final: 0.8132 (pp) REVERT: X 72 MET cc_start: 0.8792 (tmm) cc_final: 0.8349 (tmm) REVERT: X 84 LEU cc_start: 0.8558 (mp) cc_final: 0.8117 (tp) REVERT: X 92 LEU cc_start: 0.8386 (mt) cc_final: 0.7978 (mt) REVERT: X 104 MET cc_start: 0.7819 (tpt) cc_final: 0.7497 (tpt) REVERT: X 120 SER cc_start: 0.8694 (t) cc_final: 0.8472 (p) REVERT: X 223 GLU cc_start: 0.8948 (tp30) cc_final: 0.8503 (tp30) REVERT: X 224 PHE cc_start: 0.7611 (t80) cc_final: 0.7374 (t80) REVERT: X 236 ILE cc_start: 0.9049 (mm) cc_final: 0.8605 (tp) REVERT: Z 78 LYS cc_start: 0.8344 (tttt) cc_final: 0.8063 (tptp) REVERT: 7 116 ASP cc_start: 0.8071 (t0) cc_final: 0.7746 (m-30) REVERT: 7 130 PHE cc_start: 0.7005 (p90) cc_final: 0.6482 (p90) REVERT: 7 173 MET cc_start: 0.5305 (pmm) cc_final: 0.4724 (pmm) REVERT: U 68 HIS cc_start: 0.7721 (m90) cc_final: 0.7358 (t-170) REVERT: J 2 LEU cc_start: 0.7378 (mt) cc_final: 0.6954 (mt) REVERT: J 27 MET cc_start: 0.7772 (tpp) cc_final: 0.7177 (tmm) outliers start: 3 outliers final: 0 residues processed: 520 average time/residue: 0.1839 time to fit residues: 136.3020 Evaluate side-chains 429 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 11 ASN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9599 Z= 0.216 Angle : 1.180 28.319 13029 Z= 0.463 Chirality : 0.109 2.091 1638 Planarity : 0.005 0.040 1561 Dihedral : 25.947 179.198 1404 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.96 % Favored : 93.88 % Rotamer: Outliers : 0.32 % Allowed : 5.76 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.23), residues: 1192 helix: -1.02 (0.16), residues: 970 sheet: None (None), residues: 0 loop : -2.58 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP X 126 HIS 0.002 0.001 HIS U 29 PHE 0.030 0.002 PHE 8 31 TYR 0.020 0.002 TYR X 241 ARG 0.003 0.000 ARG 8 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 498 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7350 (tt) cc_final: 0.7119 (mt) REVERT: L 5 LEU cc_start: 0.7150 (pt) cc_final: 0.6879 (mp) REVERT: L 40 ASN cc_start: 0.7796 (t0) cc_final: 0.7441 (t0) REVERT: L 47 VAL cc_start: 0.8785 (t) cc_final: 0.8397 (p) REVERT: P 5 LEU cc_start: 0.8158 (pt) cc_final: 0.7885 (pt) REVERT: P 19 LEU cc_start: 0.7838 (pp) cc_final: 0.7483 (pp) REVERT: Q 5 LEU cc_start: 0.8377 (pt) cc_final: 0.7399 (mp) REVERT: Q 50 MET cc_start: 0.8483 (ptp) cc_final: 0.7644 (ptt) REVERT: Q 64 PHE cc_start: 0.7010 (m-80) cc_final: 0.6693 (m-80) REVERT: Q 67 MET cc_start: 0.7405 (ptm) cc_final: 0.7042 (tmm) REVERT: R 3 LEU cc_start: 0.6908 (tt) cc_final: 0.6225 (mt) REVERT: R 5 LEU cc_start: 0.8191 (pt) cc_final: 0.7045 (pt) REVERT: R 43 ILE cc_start: 0.8957 (tt) cc_final: 0.8681 (tt) REVERT: S 43 ILE cc_start: 0.8444 (tt) cc_final: 0.8163 (tp) REVERT: 8 10 MET cc_start: 0.6648 (mmp) cc_final: 0.5306 (mpp) REVERT: 8 31 PHE cc_start: 0.8055 (m-80) cc_final: 0.7852 (m-80) REVERT: 8 34 MET cc_start: 0.8278 (ppp) cc_final: 0.7751 (ppp) REVERT: 8 35 ILE cc_start: 0.9369 (mt) cc_final: 0.9107 (mm) REVERT: 8 37 ARG cc_start: 0.7999 (ptm160) cc_final: 0.7729 (ptm160) REVERT: X 31 LEU cc_start: 0.8586 (tt) cc_final: 0.8074 (pp) REVERT: X 72 MET cc_start: 0.8842 (tmm) cc_final: 0.8417 (tmm) REVERT: X 84 LEU cc_start: 0.8464 (mp) cc_final: 0.8113 (tp) REVERT: X 92 LEU cc_start: 0.8440 (mt) cc_final: 0.8219 (mt) REVERT: X 120 SER cc_start: 0.8683 (t) cc_final: 0.8443 (p) REVERT: X 236 ILE cc_start: 0.9028 (mm) cc_final: 0.8667 (tp) REVERT: Z 66 THR cc_start: 0.7370 (p) cc_final: 0.7165 (p) REVERT: Z 78 LYS cc_start: 0.8418 (tttt) cc_final: 0.8122 (tptm) REVERT: Z 93 ASN cc_start: 0.8221 (m-40) cc_final: 0.7812 (m-40) REVERT: 7 116 ASP cc_start: 0.8100 (t0) cc_final: 0.7812 (m-30) REVERT: 7 136 ASP cc_start: 0.8157 (m-30) cc_final: 0.7891 (m-30) REVERT: 7 173 MET cc_start: 0.5452 (pmm) cc_final: 0.5062 (pmm) REVERT: U 68 HIS cc_start: 0.7736 (m90) cc_final: 0.7342 (t-170) REVERT: J 2 LEU cc_start: 0.7612 (mt) cc_final: 0.7347 (mt) REVERT: J 27 MET cc_start: 0.7830 (tpp) cc_final: 0.7247 (tmm) outliers start: 3 outliers final: 0 residues processed: 499 average time/residue: 0.1841 time to fit residues: 130.1352 Evaluate side-chains 427 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 11 ASN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9599 Z= 0.221 Angle : 1.174 27.821 13029 Z= 0.464 Chirality : 0.109 2.092 1638 Planarity : 0.005 0.055 1561 Dihedral : 25.564 176.782 1404 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.96 % Favored : 93.88 % Rotamer: Outliers : 0.21 % Allowed : 5.01 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.24), residues: 1192 helix: -0.85 (0.16), residues: 967 sheet: None (None), residues: 0 loop : -2.27 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP X 126 HIS 0.004 0.001 HIS U 29 PHE 0.020 0.002 PHE O 64 TYR 0.025 0.002 TYR X 241 ARG 0.005 0.001 ARG Q 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 495 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7479 (tt) cc_final: 0.7019 (mt) REVERT: L 2 GLN cc_start: 0.6436 (mp10) cc_final: 0.6143 (mp10) REVERT: L 5 LEU cc_start: 0.7051 (pt) cc_final: 0.6661 (mp) REVERT: L 47 VAL cc_start: 0.8984 (t) cc_final: 0.8555 (p) REVERT: M 63 LEU cc_start: 0.9117 (mm) cc_final: 0.8807 (mm) REVERT: P 2 GLN cc_start: 0.7575 (tp40) cc_final: 0.6957 (tp40) REVERT: P 5 LEU cc_start: 0.8201 (pt) cc_final: 0.7488 (pt) REVERT: P 19 LEU cc_start: 0.7806 (pp) cc_final: 0.7504 (pp) REVERT: P 44 LYS cc_start: 0.7992 (tptt) cc_final: 0.7754 (tptt) REVERT: Q 5 LEU cc_start: 0.8464 (pt) cc_final: 0.7381 (mp) REVERT: Q 17 ILE cc_start: 0.7961 (pt) cc_final: 0.7753 (pt) REVERT: Q 50 MET cc_start: 0.8627 (ptp) cc_final: 0.7945 (ptt) REVERT: Q 67 MET cc_start: 0.7235 (ptm) cc_final: 0.7019 (tmm) REVERT: Q 71 LEU cc_start: 0.6687 (mt) cc_final: 0.6449 (mt) REVERT: R 3 LEU cc_start: 0.6962 (tt) cc_final: 0.6302 (mt) REVERT: R 43 ILE cc_start: 0.8895 (tt) cc_final: 0.8656 (tt) REVERT: 8 10 MET cc_start: 0.6237 (mmp) cc_final: 0.5513 (mpp) REVERT: 8 25 ILE cc_start: 0.9081 (mt) cc_final: 0.8676 (mt) REVERT: 8 29 GLN cc_start: 0.8132 (mp10) cc_final: 0.7882 (mp10) REVERT: 8 34 MET cc_start: 0.8249 (ppp) cc_final: 0.7715 (ppp) REVERT: 8 35 ILE cc_start: 0.9390 (mt) cc_final: 0.9175 (mm) REVERT: X 31 LEU cc_start: 0.8630 (tt) cc_final: 0.8085 (pp) REVERT: X 32 TYR cc_start: 0.6721 (m-10) cc_final: 0.6396 (m-80) REVERT: X 72 MET cc_start: 0.8898 (tmm) cc_final: 0.8384 (tmm) REVERT: X 81 ASN cc_start: 0.8349 (p0) cc_final: 0.8143 (p0) REVERT: X 84 LEU cc_start: 0.8512 (mp) cc_final: 0.8139 (tp) REVERT: X 85 TYR cc_start: 0.8168 (m-80) cc_final: 0.7922 (m-80) REVERT: X 92 LEU cc_start: 0.8504 (mt) cc_final: 0.8254 (mt) REVERT: X 230 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7662 (mm-40) REVERT: X 236 ILE cc_start: 0.9066 (mm) cc_final: 0.8716 (tp) REVERT: 7 116 ASP cc_start: 0.8220 (t0) cc_final: 0.7852 (m-30) REVERT: 7 169 ASN cc_start: 0.6200 (t0) cc_final: 0.4211 (t0) REVERT: 7 173 MET cc_start: 0.5458 (pmm) cc_final: 0.5227 (pmm) REVERT: U 68 HIS cc_start: 0.7596 (m90) cc_final: 0.7247 (t-170) REVERT: J 2 LEU cc_start: 0.7676 (mt) cc_final: 0.7384 (mt) REVERT: J 27 MET cc_start: 0.7670 (tpp) cc_final: 0.7157 (tmm) outliers start: 2 outliers final: 0 residues processed: 496 average time/residue: 0.1860 time to fit residues: 130.6522 Evaluate side-chains 417 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 0.0030 overall best weight: 0.4428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 100 ASN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9599 Z= 0.209 Angle : 1.183 27.721 13029 Z= 0.467 Chirality : 0.108 2.090 1638 Planarity : 0.005 0.059 1561 Dihedral : 25.335 177.743 1404 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.96 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.24), residues: 1192 helix: -0.75 (0.16), residues: 982 sheet: None (None), residues: 0 loop : -2.39 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 67 HIS 0.003 0.001 HIS U 29 PHE 0.034 0.002 PHE T 70 TYR 0.023 0.002 TYR X 241 ARG 0.007 0.001 ARG 7 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7433 (tt) cc_final: 0.7161 (mt) REVERT: L 2 GLN cc_start: 0.6302 (mp10) cc_final: 0.6000 (mp10) REVERT: L 5 LEU cc_start: 0.7192 (pt) cc_final: 0.6854 (mp) REVERT: L 47 VAL cc_start: 0.8902 (t) cc_final: 0.8518 (p) REVERT: N 39 ARG cc_start: 0.7259 (ptt180) cc_final: 0.6846 (ptt180) REVERT: O 50 MET cc_start: 0.7801 (ptm) cc_final: 0.7311 (mpp) REVERT: P 2 GLN cc_start: 0.7678 (tp40) cc_final: 0.7381 (tp40) REVERT: P 19 LEU cc_start: 0.7800 (pp) cc_final: 0.7403 (pp) REVERT: P 44 LYS cc_start: 0.8002 (tptt) cc_final: 0.7693 (tptt) REVERT: Q 5 LEU cc_start: 0.8322 (pt) cc_final: 0.7321 (mp) REVERT: Q 50 MET cc_start: 0.8600 (ptp) cc_final: 0.7864 (ptt) REVERT: Q 67 MET cc_start: 0.7221 (ptm) cc_final: 0.6947 (tmm) REVERT: Q 71 LEU cc_start: 0.6562 (mt) cc_final: 0.6274 (mt) REVERT: R 3 LEU cc_start: 0.6928 (tt) cc_final: 0.6280 (mt) REVERT: R 43 ILE cc_start: 0.8888 (tt) cc_final: 0.8671 (tt) REVERT: 8 34 MET cc_start: 0.8332 (ppp) cc_final: 0.7831 (ppp) REVERT: 8 35 ILE cc_start: 0.9369 (mt) cc_final: 0.9132 (mm) REVERT: X 31 LEU cc_start: 0.8404 (tt) cc_final: 0.7815 (pp) REVERT: X 72 MET cc_start: 0.8916 (tmm) cc_final: 0.8508 (tmm) REVERT: X 84 LEU cc_start: 0.8501 (mp) cc_final: 0.8151 (tp) REVERT: X 169 ARG cc_start: 0.6386 (ttm170) cc_final: 0.5345 (mtt180) REVERT: X 230 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7718 (mm-40) REVERT: X 236 ILE cc_start: 0.9039 (mm) cc_final: 0.8731 (tp) REVERT: Z 66 THR cc_start: 0.7398 (p) cc_final: 0.7154 (p) REVERT: 7 116 ASP cc_start: 0.8236 (t0) cc_final: 0.7789 (m-30) REVERT: U 68 HIS cc_start: 0.7583 (m90) cc_final: 0.7248 (t-170) REVERT: J 2 LEU cc_start: 0.7641 (mt) cc_final: 0.7400 (mt) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.1848 time to fit residues: 127.9239 Evaluate side-chains 414 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN X 100 ASN X 129 ASN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9599 Z= 0.219 Angle : 1.183 27.961 13029 Z= 0.468 Chirality : 0.108 2.090 1638 Planarity : 0.005 0.061 1561 Dihedral : 25.172 179.410 1404 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1192 helix: -0.62 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -2.36 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 67 HIS 0.004 0.001 HIS U 29 PHE 0.028 0.002 PHE T 70 TYR 0.023 0.002 TYR R 9 ARG 0.008 0.001 ARG U 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7541 (tt) cc_final: 0.7015 (mt) REVERT: L 2 GLN cc_start: 0.6332 (mp10) cc_final: 0.6013 (mp10) REVERT: L 5 LEU cc_start: 0.7280 (pt) cc_final: 0.6598 (mp) REVERT: L 47 VAL cc_start: 0.8851 (t) cc_final: 0.8516 (p) REVERT: M 50 MET cc_start: 0.7389 (ptp) cc_final: 0.7186 (ptp) REVERT: P 2 GLN cc_start: 0.7788 (tp40) cc_final: 0.7517 (tp40) REVERT: P 5 LEU cc_start: 0.8151 (pt) cc_final: 0.7617 (pt) REVERT: Q 5 LEU cc_start: 0.8399 (pt) cc_final: 0.7423 (mp) REVERT: Q 50 MET cc_start: 0.8545 (ptp) cc_final: 0.7921 (ptt) REVERT: Q 67 MET cc_start: 0.7208 (ptm) cc_final: 0.6854 (tmm) REVERT: Q 71 LEU cc_start: 0.6703 (mt) cc_final: 0.6361 (mt) REVERT: R 3 LEU cc_start: 0.6860 (tt) cc_final: 0.6143 (mt) REVERT: R 43 ILE cc_start: 0.8901 (tt) cc_final: 0.8647 (tt) REVERT: S 47 VAL cc_start: 0.9034 (t) cc_final: 0.8642 (p) REVERT: T 48 PHE cc_start: 0.7107 (t80) cc_final: 0.6532 (t80) REVERT: 8 34 MET cc_start: 0.8143 (ppp) cc_final: 0.7783 (ppp) REVERT: X 31 LEU cc_start: 0.8508 (tt) cc_final: 0.7966 (pp) REVERT: X 72 MET cc_start: 0.8933 (tmm) cc_final: 0.8330 (tmm) REVERT: X 84 LEU cc_start: 0.8572 (mp) cc_final: 0.8092 (tp) REVERT: X 85 TYR cc_start: 0.7938 (m-80) cc_final: 0.7655 (m-80) REVERT: X 88 MET cc_start: 0.7851 (tpp) cc_final: 0.7486 (tpt) REVERT: X 100 ASN cc_start: 0.8436 (m-40) cc_final: 0.8230 (m110) REVERT: X 215 MET cc_start: 0.5365 (ptp) cc_final: 0.4974 (mtt) REVERT: X 221 MET cc_start: 0.7655 (mmp) cc_final: 0.7401 (mmm) REVERT: X 230 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7749 (mm-40) REVERT: X 236 ILE cc_start: 0.9041 (mm) cc_final: 0.8786 (tp) REVERT: Z 66 THR cc_start: 0.7370 (p) cc_final: 0.7085 (p) REVERT: Z 93 ASN cc_start: 0.8267 (m-40) cc_final: 0.8030 (m110) REVERT: 7 112 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7822 (pttp) REVERT: 7 116 ASP cc_start: 0.8411 (t0) cc_final: 0.7905 (m-30) REVERT: 7 134 THR cc_start: 0.7730 (m) cc_final: 0.7087 (p) REVERT: 7 169 ASN cc_start: 0.6649 (t0) cc_final: 0.5076 (t0) REVERT: 7 173 MET cc_start: 0.5297 (pmm) cc_final: 0.4758 (pmm) REVERT: U 68 HIS cc_start: 0.7612 (m90) cc_final: 0.7206 (t-170) REVERT: J 2 LEU cc_start: 0.7734 (mt) cc_final: 0.7491 (mt) REVERT: J 13 TYR cc_start: 0.6825 (m-10) cc_final: 0.6380 (m-10) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.1734 time to fit residues: 121.2262 Evaluate side-chains 415 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 11 ASN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9599 Z= 0.226 Angle : 1.187 27.869 13029 Z= 0.471 Chirality : 0.108 2.090 1638 Planarity : 0.005 0.065 1561 Dihedral : 25.076 179.752 1404 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.24), residues: 1192 helix: -0.73 (0.16), residues: 984 sheet: None (None), residues: 0 loop : -2.18 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP X 126 HIS 0.004 0.001 HIS U 29 PHE 0.043 0.002 PHE T 70 TYR 0.023 0.002 TYR X 241 ARG 0.009 0.001 ARG U 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7438 (tt) cc_final: 0.6927 (mt) REVERT: L 2 GLN cc_start: 0.5982 (mp10) cc_final: 0.5701 (mp10) REVERT: L 5 LEU cc_start: 0.7308 (pt) cc_final: 0.6862 (mp) REVERT: L 47 VAL cc_start: 0.8893 (t) cc_final: 0.8646 (p) REVERT: P 5 LEU cc_start: 0.8072 (pt) cc_final: 0.7487 (pt) REVERT: Q 5 LEU cc_start: 0.8456 (pt) cc_final: 0.7284 (mp) REVERT: Q 50 MET cc_start: 0.8546 (ptp) cc_final: 0.7936 (ptt) REVERT: Q 67 MET cc_start: 0.7168 (ptm) cc_final: 0.6871 (tmm) REVERT: Q 71 LEU cc_start: 0.6651 (mt) cc_final: 0.6288 (mt) REVERT: R 3 LEU cc_start: 0.6850 (tt) cc_final: 0.6159 (mt) REVERT: R 43 ILE cc_start: 0.8893 (tt) cc_final: 0.8639 (tt) REVERT: S 43 ILE cc_start: 0.8507 (tp) cc_final: 0.8290 (tp) REVERT: S 47 VAL cc_start: 0.9075 (t) cc_final: 0.8419 (p) REVERT: S 57 LEU cc_start: 0.8601 (mt) cc_final: 0.8370 (mp) REVERT: T 48 PHE cc_start: 0.7194 (t80) cc_final: 0.6496 (t80) REVERT: 8 34 MET cc_start: 0.8111 (ppp) cc_final: 0.7813 (ppp) REVERT: X 31 LEU cc_start: 0.8504 (tt) cc_final: 0.8032 (pp) REVERT: X 32 TYR cc_start: 0.6678 (m-10) cc_final: 0.6311 (m-80) REVERT: X 72 MET cc_start: 0.8924 (tmm) cc_final: 0.8422 (tmm) REVERT: X 84 LEU cc_start: 0.8330 (mp) cc_final: 0.8001 (tp) REVERT: X 85 TYR cc_start: 0.8090 (m-80) cc_final: 0.7829 (m-80) REVERT: X 88 MET cc_start: 0.7830 (tpp) cc_final: 0.7571 (tpt) REVERT: X 215 MET cc_start: 0.6323 (ptp) cc_final: 0.5695 (mtt) REVERT: X 221 MET cc_start: 0.7812 (mmp) cc_final: 0.7558 (mmm) REVERT: X 230 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7621 (mm-40) REVERT: X 236 ILE cc_start: 0.9080 (mm) cc_final: 0.8802 (tp) REVERT: Z 66 THR cc_start: 0.7462 (p) cc_final: 0.7169 (p) REVERT: 7 112 LYS cc_start: 0.8187 (tmtt) cc_final: 0.7828 (pttp) REVERT: 7 116 ASP cc_start: 0.8385 (t0) cc_final: 0.7907 (m-30) REVERT: 7 169 ASN cc_start: 0.6778 (t0) cc_final: 0.5238 (t0) REVERT: 7 173 MET cc_start: 0.5128 (pmm) cc_final: 0.4663 (pmm) REVERT: U 68 HIS cc_start: 0.7754 (m90) cc_final: 0.7258 (t-170) REVERT: J 2 LEU cc_start: 0.7716 (mt) cc_final: 0.7358 (mt) REVERT: J 13 TYR cc_start: 0.6884 (m-10) cc_final: 0.6450 (m-10) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.1739 time to fit residues: 120.5509 Evaluate side-chains 404 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.0870 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 ASN 8 11 ASN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 100 ASN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9599 Z= 0.221 Angle : 1.198 27.789 13029 Z= 0.475 Chirality : 0.108 2.090 1638 Planarity : 0.005 0.065 1561 Dihedral : 24.990 179.439 1404 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.24), residues: 1192 helix: -0.72 (0.17), residues: 967 sheet: None (None), residues: 0 loop : -2.24 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP X 126 HIS 0.003 0.000 HIS U 29 PHE 0.044 0.002 PHE T 70 TYR 0.024 0.002 TYR X 241 ARG 0.008 0.001 ARG U 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7295 (tt) cc_final: 0.6880 (mt) REVERT: L 2 GLN cc_start: 0.6106 (mp10) cc_final: 0.5800 (mp10) REVERT: L 5 LEU cc_start: 0.7366 (pt) cc_final: 0.6794 (mp) REVERT: L 47 VAL cc_start: 0.8724 (t) cc_final: 0.8450 (p) REVERT: M 43 ILE cc_start: 0.8750 (tp) cc_final: 0.8541 (tt) REVERT: P 2 GLN cc_start: 0.8169 (tp40) cc_final: 0.7636 (tp40) REVERT: P 5 LEU cc_start: 0.7982 (pt) cc_final: 0.7570 (pt) REVERT: Q 5 LEU cc_start: 0.8363 (pt) cc_final: 0.7221 (mp) REVERT: Q 47 VAL cc_start: 0.8468 (p) cc_final: 0.8039 (p) REVERT: Q 50 MET cc_start: 0.8510 (ptp) cc_final: 0.8058 (ptt) REVERT: Q 67 MET cc_start: 0.7165 (ptm) cc_final: 0.6913 (tmm) REVERT: Q 71 LEU cc_start: 0.6806 (mt) cc_final: 0.6425 (mt) REVERT: Q 72 LEU cc_start: 0.7521 (tp) cc_final: 0.7302 (tp) REVERT: R 3 LEU cc_start: 0.6849 (tt) cc_final: 0.6176 (mt) REVERT: R 43 ILE cc_start: 0.8812 (tt) cc_final: 0.8610 (tt) REVERT: S 57 LEU cc_start: 0.8549 (mt) cc_final: 0.8302 (mp) REVERT: T 48 PHE cc_start: 0.7099 (t80) cc_final: 0.6692 (t80) REVERT: 8 34 MET cc_start: 0.8110 (ppp) cc_final: 0.7863 (ppp) REVERT: X 31 LEU cc_start: 0.8438 (tt) cc_final: 0.7981 (pp) REVERT: X 32 TYR cc_start: 0.6634 (m-10) cc_final: 0.6329 (m-80) REVERT: X 72 MET cc_start: 0.8975 (tmm) cc_final: 0.8467 (tmm) REVERT: X 84 LEU cc_start: 0.8273 (mp) cc_final: 0.8014 (tp) REVERT: X 86 PHE cc_start: 0.8646 (t80) cc_final: 0.8408 (t80) REVERT: X 88 MET cc_start: 0.7769 (tpp) cc_final: 0.7513 (tpt) REVERT: X 100 ASN cc_start: 0.8467 (m-40) cc_final: 0.8264 (m110) REVERT: X 215 MET cc_start: 0.6424 (ptp) cc_final: 0.5628 (mtt) REVERT: X 230 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7755 (mm-40) REVERT: Z 66 THR cc_start: 0.7386 (p) cc_final: 0.7150 (p) REVERT: 7 112 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7833 (pttp) REVERT: 7 116 ASP cc_start: 0.8382 (t0) cc_final: 0.7908 (m-30) REVERT: 7 169 ASN cc_start: 0.6887 (t0) cc_final: 0.4952 (t0) REVERT: 7 173 MET cc_start: 0.5081 (pmm) cc_final: 0.4692 (pmm) REVERT: U 68 HIS cc_start: 0.7717 (m90) cc_final: 0.7249 (t-170) REVERT: J 2 LEU cc_start: 0.7683 (mt) cc_final: 0.7452 (mt) REVERT: J 13 TYR cc_start: 0.6814 (m-10) cc_final: 0.6315 (m-10) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.1752 time to fit residues: 118.8730 Evaluate side-chains 408 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN R 35 ASN 8 11 ASN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9599 Z= 0.219 Angle : 1.195 27.746 13029 Z= 0.474 Chirality : 0.108 2.090 1638 Planarity : 0.005 0.066 1561 Dihedral : 24.871 179.135 1404 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1192 helix: -0.67 (0.16), residues: 982 sheet: None (None), residues: 0 loop : -2.21 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP U 67 HIS 0.003 0.001 HIS U 29 PHE 0.039 0.002 PHE T 70 TYR 0.019 0.001 TYR X 241 ARG 0.009 0.001 ARG U 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7371 (tt) cc_final: 0.6904 (mt) REVERT: L 5 LEU cc_start: 0.7382 (pt) cc_final: 0.6955 (mp) REVERT: L 47 VAL cc_start: 0.8606 (t) cc_final: 0.8360 (p) REVERT: M 43 ILE cc_start: 0.8811 (tp) cc_final: 0.8603 (tt) REVERT: M 44 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7721 (tptt) REVERT: O 73 LEU cc_start: 0.7663 (tt) cc_final: 0.7323 (mt) REVERT: P 2 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7816 (tp40) REVERT: P 5 LEU cc_start: 0.8035 (pt) cc_final: 0.7647 (pt) REVERT: P 50 MET cc_start: 0.8110 (ptp) cc_final: 0.7676 (ptt) REVERT: Q 5 LEU cc_start: 0.8384 (pt) cc_final: 0.7258 (mp) REVERT: Q 50 MET cc_start: 0.8493 (ptp) cc_final: 0.8045 (ptt) REVERT: Q 67 MET cc_start: 0.7330 (ptm) cc_final: 0.7117 (tmm) REVERT: Q 71 LEU cc_start: 0.6741 (mt) cc_final: 0.6386 (mt) REVERT: R 3 LEU cc_start: 0.6860 (tt) cc_final: 0.6147 (mt) REVERT: R 43 ILE cc_start: 0.8797 (tt) cc_final: 0.8582 (tt) REVERT: S 34 ILE cc_start: 0.9422 (mt) cc_final: 0.9156 (tp) REVERT: S 47 VAL cc_start: 0.8978 (t) cc_final: 0.8716 (t) REVERT: S 57 LEU cc_start: 0.8534 (mt) cc_final: 0.8297 (mp) REVERT: T 48 PHE cc_start: 0.7040 (t80) cc_final: 0.6720 (t80) REVERT: T 72 LEU cc_start: 0.8258 (tp) cc_final: 0.8052 (tp) REVERT: 8 29 GLN cc_start: 0.8389 (mp10) cc_final: 0.8158 (mp10) REVERT: 8 34 MET cc_start: 0.8101 (ppp) cc_final: 0.7831 (ppp) REVERT: X 72 MET cc_start: 0.8887 (tmm) cc_final: 0.8627 (tmm) REVERT: X 84 LEU cc_start: 0.8292 (mp) cc_final: 0.8022 (tp) REVERT: X 85 TYR cc_start: 0.8075 (m-80) cc_final: 0.7831 (m-80) REVERT: X 88 MET cc_start: 0.7779 (tpp) cc_final: 0.7565 (tpt) REVERT: X 188 MET cc_start: 0.7322 (mmt) cc_final: 0.6968 (mmt) REVERT: X 215 MET cc_start: 0.6385 (ptp) cc_final: 0.5655 (mtt) REVERT: X 230 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7613 (mm-40) REVERT: X 233 VAL cc_start: 0.9292 (t) cc_final: 0.8826 (t) REVERT: Z 66 THR cc_start: 0.7403 (p) cc_final: 0.7179 (p) REVERT: 7 169 ASN cc_start: 0.6957 (t0) cc_final: 0.5358 (t0) REVERT: 7 173 MET cc_start: 0.4960 (pmm) cc_final: 0.4682 (pmm) REVERT: U 68 HIS cc_start: 0.7639 (m90) cc_final: 0.7227 (t-170) REVERT: J 2 LEU cc_start: 0.7657 (mt) cc_final: 0.7430 (mt) REVERT: J 13 TYR cc_start: 0.6799 (m-10) cc_final: 0.6389 (m-10) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.1730 time to fit residues: 118.2986 Evaluate side-chains 406 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.0870 chunk 28 optimal weight: 7.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 11 ASN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN X 100 ASN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9599 Z= 0.226 Angle : 1.208 27.843 13029 Z= 0.478 Chirality : 0.108 2.090 1638 Planarity : 0.005 0.068 1561 Dihedral : 24.791 179.261 1404 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1192 helix: -0.62 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -1.91 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP U 67 HIS 0.003 0.001 HIS U 29 PHE 0.031 0.002 PHE T 70 TYR 0.028 0.002 TYR X 241 ARG 0.003 0.000 ARG O 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LEU cc_start: 0.7359 (tt) cc_final: 0.6864 (mt) REVERT: L 5 LEU cc_start: 0.7446 (pt) cc_final: 0.6879 (mp) REVERT: M 44 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7687 (tptt) REVERT: M 50 MET cc_start: 0.6755 (ptp) cc_final: 0.6098 (ptt) REVERT: M 53 LEU cc_start: 0.9175 (tt) cc_final: 0.8459 (mt) REVERT: O 73 LEU cc_start: 0.7690 (tt) cc_final: 0.7324 (mt) REVERT: P 2 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7753 (tp-100) REVERT: P 5 LEU cc_start: 0.8023 (pt) cc_final: 0.7609 (pt) REVERT: P 50 MET cc_start: 0.8073 (ptp) cc_final: 0.7406 (ptt) REVERT: Q 47 VAL cc_start: 0.8511 (p) cc_final: 0.8021 (p) REVERT: Q 50 MET cc_start: 0.8454 (ptp) cc_final: 0.8060 (ptt) REVERT: Q 67 MET cc_start: 0.7317 (ptm) cc_final: 0.7109 (tmm) REVERT: Q 71 LEU cc_start: 0.6771 (mt) cc_final: 0.6399 (mt) REVERT: Q 72 LEU cc_start: 0.7392 (tp) cc_final: 0.7081 (tp) REVERT: R 3 LEU cc_start: 0.6561 (tt) cc_final: 0.5980 (mt) REVERT: R 43 ILE cc_start: 0.8788 (tt) cc_final: 0.8583 (tt) REVERT: S 34 ILE cc_start: 0.9389 (mt) cc_final: 0.8958 (tp) REVERT: S 47 VAL cc_start: 0.9020 (t) cc_final: 0.8727 (t) REVERT: S 57 LEU cc_start: 0.8514 (mt) cc_final: 0.8302 (mp) REVERT: T 48 PHE cc_start: 0.7165 (t80) cc_final: 0.6712 (t80) REVERT: 8 29 GLN cc_start: 0.8342 (mp10) cc_final: 0.8117 (mp10) REVERT: 8 34 MET cc_start: 0.8139 (ppp) cc_final: 0.7878 (ppp) REVERT: X 54 ILE cc_start: 0.8659 (mm) cc_final: 0.8451 (mm) REVERT: X 72 MET cc_start: 0.8885 (tmm) cc_final: 0.8442 (tmm) REVERT: X 84 LEU cc_start: 0.8250 (mp) cc_final: 0.8030 (tp) REVERT: X 85 TYR cc_start: 0.8060 (m-80) cc_final: 0.7819 (m-80) REVERT: X 100 ASN cc_start: 0.8538 (m-40) cc_final: 0.8284 (m110) REVERT: X 188 MET cc_start: 0.7262 (mmt) cc_final: 0.6793 (mpp) REVERT: X 215 MET cc_start: 0.6395 (ptp) cc_final: 0.5756 (mtt) REVERT: X 230 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7708 (mm-40) REVERT: X 234 TRP cc_start: 0.7879 (t-100) cc_final: 0.7639 (t-100) REVERT: X 236 ILE cc_start: 0.9109 (mm) cc_final: 0.8831 (tp) REVERT: Z 66 THR cc_start: 0.7202 (p) cc_final: 0.6945 (p) REVERT: 7 116 ASP cc_start: 0.8359 (t0) cc_final: 0.7887 (m-30) REVERT: 7 169 ASN cc_start: 0.6995 (t0) cc_final: 0.5351 (t0) REVERT: 7 173 MET cc_start: 0.5191 (pmm) cc_final: 0.4728 (pmm) REVERT: J 2 LEU cc_start: 0.7662 (mt) cc_final: 0.7405 (mt) REVERT: J 13 TYR cc_start: 0.6849 (m-10) cc_final: 0.6434 (m-10) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.1716 time to fit residues: 115.5290 Evaluate side-chains 406 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 11 ASN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.144905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127473 restraints weight = 23757.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.129892 restraints weight = 15892.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.131598 restraints weight = 11749.666| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9599 Z= 0.226 Angle : 1.213 27.739 13029 Z= 0.484 Chirality : 0.108 2.091 1638 Planarity : 0.005 0.067 1561 Dihedral : 24.662 179.675 1404 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.25), residues: 1192 helix: -0.61 (0.17), residues: 977 sheet: None (None), residues: 0 loop : -1.82 (0.46), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP U 67 HIS 0.003 0.001 HIS U 29 PHE 0.048 0.002 PHE T 70 TYR 0.030 0.001 TYR X 241 ARG 0.003 0.000 ARG O 39 =============================================================================== Job complete usr+sys time: 2695.86 seconds wall clock time: 48 minutes 56.60 seconds (2936.60 seconds total)