Starting phenix.real_space_refine on Fri Dec 8 21:18:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/12_2023/6cp7_7549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/12_2023/6cp7_7549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/12_2023/6cp7_7549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/12_2023/6cp7_7549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/12_2023/6cp7_7549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/12_2023/6cp7_7549_updated.pdb" } resolution = 4.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 6129 2.51 5 N 1423 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 59": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9164 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 534 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" 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: "M" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 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: "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: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1760 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 393 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 52} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 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} Time building chain proxies: 5.38, per 1000 atoms: 0.59 Number of scatterers: 9164 At special positions: 0 Unit cell: (84.87, 113.16, 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 1561 8.00 N 1423 7.00 C 6129 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: 3.87 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: 56 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'K' and resid 3 through 16 removed outlier: 4.048A pdb=" N THR K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 37 removed outlier: 3.875A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 58 removed outlier: 4.904A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 4.095A pdb=" N PHE K 55 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU K 57 " --> pdb=" O GLY K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 73 removed outlier: 4.477A pdb=" N LEU K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU K 71 " --> pdb=" O VAL K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 14 Processing helix chain 'L' and resid 17 through 37 removed outlier: 3.646A pdb=" N LEU L 20 " --> pdb=" O ILE L 17 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE L 24 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY L 25 " --> pdb=" O ALA L 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN L 35 " --> pdb=" O ALA L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 72 removed outlier: 3.901A pdb=" N LYS L 44 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP L 45 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE L 48 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Proline residue: L 49 - end of helix removed outlier: 4.998A pdb=" N LEU L 57 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA L 60 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 37 removed outlier: 4.239A pdb=" N ILE M 17 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY M 18 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 56 removed outlier: 4.043A pdb=" N LYS M 44 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP M 45 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE M 48 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Proline residue: M 49 - end of helix Processing helix chain 'M' and resid 60 through 73 removed outlier: 3.532A pdb=" N VAL M 68 " --> pdb=" O PHE M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 14 Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.812A pdb=" N ALA N 22 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE N 26 " --> pdb=" O GLY N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 73 Proline residue: N 49 - end of helix removed outlier: 4.688A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 13 Processing helix chain 'O' and resid 20 through 24 Processing helix chain 'O' and resid 26 through 37 removed outlier: 3.637A pdb=" N PHE O 30 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 73 removed outlier: 4.396A pdb=" N LYS O 44 " --> pdb=" O PRO O 41 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP O 45 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE O 48 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Proline residue: O 49 - end of helix removed outlier: 3.526A pdb=" N ALA O 56 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU O 57 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA O 60 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR O 61 " --> pdb=" O SER O 58 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU O 71 " --> pdb=" O VAL O 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 13 Processing helix chain 'P' and resid 20 through 37 removed outlier: 4.919A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 73 removed outlier: 3.829A pdb=" N THR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY P 62 " --> pdb=" O SER P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 14 Processing helix chain 'Q' and resid 16 through 18 No H-bonds generated for 'chain 'Q' and resid 16 through 18' Processing helix chain 'Q' and resid 20 through 23 No H-bonds generated for 'chain 'Q' and resid 20 through 23' Processing helix chain 'Q' and resid 25 through 36 removed outlier: 3.722A pdb=" N PHE Q 30 " --> pdb=" O ALA Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 73 removed outlier: 4.125A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.694A pdb=" N THR R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 39 removed outlier: 3.860A pdb=" N ALA R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 56 removed outlier: 3.563A pdb=" N LYS R 44 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASP R 45 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Proline residue: R 49 - end of helix Processing helix chain 'R' and resid 59 through 74 removed outlier: 3.517A pdb=" N CYS R 65 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU R 73 " --> pdb=" O SER R 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 14 Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 20 through 38 removed outlier: 4.301A pdb=" N ALA S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE S 28 " --> pdb=" O ILE S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 48 through 73 removed outlier: 3.853A pdb=" N GLY S 54 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS S 65 " --> pdb=" O THR S 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 14 Processing helix chain 'T' and resid 17 through 37 removed outlier: 3.637A pdb=" N LEU T 20 " --> pdb=" O ILE T 17 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE T 24 " --> pdb=" O GLY T 21 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE T 26 " --> pdb=" O GLY T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 61 removed outlier: 3.917A pdb=" N LYS T 44 " --> pdb=" O PRO T 41 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP T 45 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL T 47 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE T 48 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Proline residue: T 49 - end of helix removed outlier: 4.291A pdb=" N ILE T 52 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA T 60 " --> pdb=" O LEU T 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR T 61 " --> pdb=" O SER T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 71 Processing helix chain '8' and resid 9 through 46 removed outlier: 5.037A pdb=" N LEU 8 32 " --> pdb=" O SER 8 28 " (cutoff:3.500A) Proline residue: 8 33 - end of helix removed outlier: 3.879A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 43 Processing helix chain 'X' and resid 57 through 76 removed outlier: 3.918A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 102 removed outlier: 3.829A pdb=" N PHE X 93 " --> pdb=" O ILE X 89 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE X 95 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN X 100 " --> pdb=" O ILE X 96 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU X 101 " --> pdb=" O PHE X 97 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 137 Processing helix chain 'X' and resid 140 through 144 Processing helix chain 'X' and resid 152 through 161 Proline residue: X 156 - end of helix Processing helix chain 'X' and resid 163 through 199 removed outlier: 4.285A pdb=" N ALA X 170 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE X 171 " --> pdb=" O PHE X 167 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 206 removed outlier: 3.757A pdb=" N LEU X 206 " --> pdb=" O LEU X 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 203 through 206' Processing helix chain 'X' and resid 211 through 246 removed outlier: 3.592A pdb=" N ALA X 225 " --> pdb=" O MET X 221 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 105 removed outlier: 3.808A pdb=" N LEU Z 58 " --> pdb=" O ASP Z 54 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.955A pdb=" N LYS Z 104 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP Z 105 " --> pdb=" O GLU Z 101 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 124 removed outlier: 4.863A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU 7 117 " --> pdb=" O GLU 7 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN 7 118 " --> pdb=" O LEU 7 114 " (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 Processing helix chain 'U' and resid 49 through 55 Processing helix chain 'U' and resid 64 through 84 removed outlier: 4.173A pdb=" N TYR U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 626 hydrogen bonds defined for protein. 1479 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: 2.37 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2542 1.34 - 1.46: 1979 1.46 - 1.58: 4728 1.58 - 1.70: 0 1.70 - 1.81: 92 Bond restraints: 9341 Sorted by residual: bond pdb=" C PHE R 48 " pdb=" N PRO R 49 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C LEU X 152 " pdb=" N PRO X 153 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.01e+00 bond pdb=" C PHE M 48 " pdb=" N PRO M 49 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.30e-02 5.92e+03 7.18e+00 bond pdb=" SD FME K 1 " pdb=" CE FME K 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" SD FME P 1 " pdb=" CE FME P 1 " ideal model delta sigma weight residual 1.805 1.754 0.051 2.00e-02 2.50e+03 6.48e+00 ... (remaining 9336 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.79: 153 104.79 - 112.13: 4397 112.13 - 119.46: 3390 119.46 - 126.80: 4634 126.80 - 134.14: 80 Bond angle restraints: 12654 Sorted by residual: angle pdb=" N GLU O 59 " pdb=" CA GLU O 59 " pdb=" C GLU O 59 " ideal model delta sigma weight residual 112.23 105.24 6.99 1.26e+00 6.30e-01 3.08e+01 angle pdb=" O VAL X 155 " pdb=" C VAL X 155 " pdb=" N PRO X 156 " ideal model delta sigma weight residual 120.42 123.94 -3.52 6.40e-01 2.44e+00 3.03e+01 angle pdb=" N GLY S 25 " pdb=" CA GLY S 25 " pdb=" C GLY S 25 " ideal model delta sigma weight residual 112.49 118.90 -6.41 1.21e+00 6.83e-01 2.80e+01 angle pdb=" N GLY T 25 " pdb=" CA GLY T 25 " pdb=" C GLY T 25 " ideal model delta sigma weight residual 112.49 118.72 -6.23 1.21e+00 6.83e-01 2.65e+01 angle pdb=" C ASN X 49 " pdb=" N ASN X 50 " pdb=" CA ASN X 50 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 ... (remaining 12649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4972 17.62 - 35.23: 344 35.23 - 52.85: 63 52.85 - 70.46: 11 70.46 - 88.08: 4 Dihedral angle restraints: 5394 sinusoidal: 1915 harmonic: 3479 Sorted by residual: dihedral pdb=" CA ALA U 75 " pdb=" C ALA U 75 " pdb=" N PHE U 76 " pdb=" CA PHE U 76 " ideal model delta harmonic sigma weight residual 180.00 -148.68 -31.32 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA LEU R 19 " pdb=" C LEU R 19 " pdb=" N LEU R 20 " pdb=" CA LEU R 20 " ideal model delta harmonic sigma weight residual 180.00 149.12 30.88 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA LEU M 19 " pdb=" C LEU M 19 " pdb=" N LEU M 20 " pdb=" CA LEU M 20 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 5391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1366 0.098 - 0.196: 172 0.196 - 0.293: 15 0.293 - 0.391: 3 0.391 - 0.489: 2 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CB ILE O 14 " pdb=" CA ILE O 14 " pdb=" CG1 ILE O 14 " pdb=" CG2 ILE O 14 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" CB ILE P 14 " pdb=" CA ILE P 14 " pdb=" CG1 ILE P 14 " pdb=" CG2 ILE P 14 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE K 28 " pdb=" CA ILE K 28 " pdb=" CG1 ILE K 28 " pdb=" CG2 ILE K 28 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 1555 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 40 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO L 41 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO L 41 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 41 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 31 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ALA M 31 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA M 31 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA M 32 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE N 28 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C ILE N 28 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE N 28 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL N 29 " 0.017 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 54 2.48 - 3.09: 6604 3.09 - 3.69: 15175 3.69 - 4.30: 21278 4.30 - 4.90: 32995 Nonbonded interactions: 76106 Sorted by model distance: nonbonded pdb=" O LEU X 164 " pdb=" CB ALA X 168 " model vdw 1.876 2.768 nonbonded pdb=" O ILE Q 24 " pdb=" N ILE Q 26 " model vdw 1.947 2.520 nonbonded pdb=" O SER M 58 " pdb=" N ALA M 60 " model vdw 2.043 2.520 nonbonded pdb=" O GLY Q 54 " pdb=" CB SER Q 58 " model vdw 2.084 2.752 nonbonded pdb=" CG2 ILE Q 24 " pdb=" N GLY Q 25 " model vdw 2.134 3.540 ... (remaining 76101 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 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 56 or (resid 57 through 58 and (name N or name CA or name C or name O or name CB \ )) or resid 59 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 'L' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 56 or (resid 57 throug \ h 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throug \ h 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or re \ sid 62 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 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 56 or (resid 57 through 58 and (name N or name CA or name C or name \ O or name CB )) or resid 59 through 74)) selection = (chain 'N' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throug \ h 56 or (resid 57 through 58 and (name N or name CA or name C or name O or name \ CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 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 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 56 or (resid 57 through 58 and (name N or name CA or name C or name \ O or name CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or n \ ame C or name O or name CB )) or resid 62 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 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 41 or (resid 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 57 or (resi \ d 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throug \ h 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or re \ sid 62 through 74)) selection = (chain 'Q' and (resid 1 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 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 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 57 or (resid 58 and (name N or name CA or name C or name O or name \ CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 through 74)) selection = (chain 'S' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throug \ h 56 or (resid 57 through 58 and (name N or name CA or name C or name O or name \ CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 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 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 56 or (resid 57 through 58 and (name N or name CA or name C or name \ O or name CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or n \ ame C or name O or name CB )) or resid 62 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: 1.840 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: 7.460 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.260 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 : 0.008 0.099 9341 Z= 0.526 Angle : 1.418 15.141 12654 Z= 0.741 Chirality : 0.068 0.489 1558 Planarity : 0.009 0.087 1537 Dihedral : 13.158 88.077 3168 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.63 % Favored : 92.87 % Rotamer: Outliers : 3.98 % Allowed : 11.41 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.99 (0.18), residues: 1192 helix: -3.07 (0.12), residues: 947 sheet: None (None), residues: 0 loop : -3.16 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP X 234 HIS 0.012 0.003 HIS X 114 PHE 0.034 0.004 PHE X 224 TYR 0.026 0.003 TYR U 51 ARG 0.011 0.001 ARG X 176 *********************** 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 554 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 517 time to evaluate : 1.111 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 outliers start: 37 outliers final: 15 residues processed: 533 average time/residue: 0.1835 time to fit residues: 137.3211 Evaluate side-chains 399 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 384 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0894 time to fit residues: 3.6345 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 90 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN U 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9341 Z= 0.233 Angle : 0.843 10.405 12654 Z= 0.410 Chirality : 0.043 0.289 1558 Planarity : 0.006 0.058 1537 Dihedral : 6.676 54.406 1276 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.54 % Allowed : 5.81 % Favored : 93.65 % 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: -3.23 (0.21), residues: 1192 helix: -1.73 (0.15), residues: 951 sheet: None (None), residues: 0 loop : -3.01 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 234 HIS 0.007 0.002 HIS X 185 PHE 0.029 0.002 PHE Q 64 TYR 0.025 0.002 TYR X 44 ARG 0.006 0.001 ARG X 169 *********************** 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 479 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 474 time to evaluate : 1.015 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 outliers start: 5 outliers final: 2 residues processed: 477 average time/residue: 0.1790 time to fit residues: 120.8723 Evaluate side-chains 389 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0831 time to fit residues: 1.6520 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 8.9990 chunk 87 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 35 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9341 Z= 0.218 Angle : 0.788 12.097 12654 Z= 0.376 Chirality : 0.043 0.244 1558 Planarity : 0.005 0.060 1537 Dihedral : 6.007 49.693 1276 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.32 % Allowed : 5.17 % Favored : 94.51 % 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: -2.00 (0.23), residues: 1192 helix: -0.87 (0.16), residues: 903 sheet: None (None), residues: 0 loop : -2.37 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.029 0.002 PHE X 224 TYR 0.011 0.001 TYR U 82 ARG 0.004 0.000 ARG X 169 *********************** 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 480 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 477 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 479 average time/residue: 0.1773 time to fit residues: 121.2805 Evaluate side-chains 385 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0869 time to fit residues: 1.5478 ------------------------------------------------------------------------------- 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: 7.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9341 Z= 0.235 Angle : 0.784 11.904 12654 Z= 0.377 Chirality : 0.043 0.238 1558 Planarity : 0.005 0.057 1537 Dihedral : 5.786 48.371 1276 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: -1.58 (0.23), residues: 1192 helix: -0.57 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -2.23 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.050 0.002 PHE Q 64 TYR 0.023 0.002 TYR O 9 ARG 0.007 0.000 ARG X 169 *********************** 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 457 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.1924 time to fit residues: 127.6424 Evaluate side-chains 380 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4056 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9341 Z= 0.268 Angle : 0.813 12.337 12654 Z= 0.391 Chirality : 0.044 0.229 1558 Planarity : 0.005 0.057 1537 Dihedral : 5.738 49.299 1276 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.11 % Allowed : 3.98 % Favored : 95.91 % 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: -1.29 (0.24), residues: 1192 helix: -0.42 (0.16), residues: 943 sheet: None (None), residues: 0 loop : -2.03 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.035 0.002 PHE X 224 TYR 0.023 0.002 TYR 8 15 ARG 0.002 0.000 ARG X 169 *********************** 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 443 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 442 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 outliers start: 1 outliers final: 1 residues processed: 442 average time/residue: 0.1720 time to fit residues: 109.8329 Evaluate side-chains 375 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1042 time to fit residues: 1.4856 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 180 ASN ** X 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9341 Z= 0.261 Angle : 0.813 12.502 12654 Z= 0.390 Chirality : 0.043 0.226 1558 Planarity : 0.004 0.054 1537 Dihedral : 5.662 49.421 1276 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.34 % 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: -1.03 (0.24), residues: 1192 helix: -0.22 (0.17), residues: 939 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.027 0.002 PHE P 64 TYR 0.033 0.002 TYR K 9 ARG 0.002 0.000 ARG 8 37 *********************** 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 446 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.1764 time to fit residues: 113.3403 Evaluate side-chains 366 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4093 ------------------------------------------------------------------------------- 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: 5.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 12 GLN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** X 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9341 Z= 0.242 Angle : 0.843 14.845 12654 Z= 0.400 Chirality : 0.043 0.211 1558 Planarity : 0.004 0.053 1537 Dihedral : 5.585 47.837 1276 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.24), residues: 1192 helix: -0.41 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -2.27 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.041 0.002 PHE X 224 TYR 0.021 0.002 TYR M 9 ARG 0.004 0.000 ARG P 39 *********************** 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 440 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1783 time to fit residues: 112.4127 Evaluate side-chains 367 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3325 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9341 Z= 0.239 Angle : 0.853 14.731 12654 Z= 0.401 Chirality : 0.044 0.299 1558 Planarity : 0.004 0.051 1537 Dihedral : 5.493 45.951 1276 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -1.14 (0.24), residues: 1192 helix: -0.35 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -2.20 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 234 HIS 0.003 0.001 HIS X 185 PHE 0.031 0.002 PHE J 16 TYR 0.020 0.002 TYR O 9 ARG 0.002 0.000 ARG P 39 *********************** 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 440 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1815 time to fit residues: 115.0770 Evaluate side-chains 367 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3431 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 0.0170 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 overall best weight: 1.0220 ------------------------------------------------------------------------------- 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 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9341 Z= 0.232 Angle : 0.866 14.321 12654 Z= 0.404 Chirality : 0.044 0.284 1558 Planarity : 0.004 0.050 1537 Dihedral : 5.471 43.276 1276 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -1.01 (0.24), residues: 1192 helix: -0.27 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -2.07 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.026 0.002 PHE S 64 TYR 0.023 0.001 TYR O 9 ARG 0.006 0.000 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 445 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1755 time to fit residues: 111.9156 Evaluate side-chains 374 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3657 ------------------------------------------------------------------------------- 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: 0.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9341 Z= 0.246 Angle : 0.855 14.885 12654 Z= 0.403 Chirality : 0.044 0.246 1558 Planarity : 0.004 0.049 1537 Dihedral : 5.444 41.802 1276 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1192 helix: -0.19 (0.17), residues: 991 sheet: None (None), residues: 0 loop : -2.06 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.028 0.002 PHE S 64 TYR 0.019 0.001 TYR O 9 ARG 0.003 0.000 ARG U 50 ********************** 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 441 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.1792 time to fit residues: 113.8144 Evaluate side-chains 363 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4658 ------------------------------------------------------------------------------- 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: 5.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.0050 chunk 92 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 129 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.132276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.112392 restraints weight = 26222.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.114098 restraints weight = 18172.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.115789 restraints weight = 13424.506| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9341 Z= 0.218 Angle : 0.865 14.750 12654 Z= 0.400 Chirality : 0.044 0.235 1558 Planarity : 0.004 0.048 1537 Dihedral : 5.340 37.540 1276 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1192 helix: -0.14 (0.17), residues: 998 sheet: None (None), residues: 0 loop : -1.74 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.027 0.002 PHE R 64 TYR 0.017 0.001 TYR X 241 ARG 0.005 0.000 ARG U 50 =============================================================================== Job complete usr+sys time: 2564.62 seconds wall clock time: 46 minutes 59.04 seconds (2819.04 seconds total)