Starting phenix.real_space_refine on Wed Feb 14 11:34:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/02_2024/6cp7_7549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/02_2024/6cp7_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_7549/02_2024/6cp7_7549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/02_2024/6cp7_7549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/02_2024/6cp7_7549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/02_2024/6cp7_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.43, 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: 3.86 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: 1.45 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: 2.50 Time building geometry restraints manager: 4.16 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: 2.290 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: 0.000 Extract box with map and model: 7.430 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.190 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.480 ------------------------------------------------------------------------------- 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 : 0.878 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 14 ILE cc_start: 0.7397 (pt) cc_final: 0.7035 (mt) REVERT: L 39 ARG cc_start: 0.7465 (ptm-80) cc_final: 0.6991 (tmt-80) REVERT: M 28 ILE cc_start: 0.9312 (pt) cc_final: 0.8968 (tt) REVERT: M 39 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6961 (tpm170) REVERT: M 59 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: M 67 MET cc_start: 0.7624 (pp-130) cc_final: 0.6720 (pp-130) REVERT: R 47 VAL cc_start: 0.8822 (m) cc_final: 0.8402 (t) REVERT: R 65 CYS cc_start: 0.7002 (t) cc_final: 0.6800 (t) REVERT: S 2 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7691 (pm20) REVERT: S 10 ILE cc_start: 0.8541 (pp) cc_final: 0.8259 (tt) REVERT: S 14 ILE cc_start: 0.9153 (pt) cc_final: 0.8516 (mt) REVERT: S 28 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8021 (pt) REVERT: S 39 ARG cc_start: 0.6827 (ppp80) cc_final: 0.5902 (tpt170) REVERT: S 66 LEU cc_start: 0.8009 (pt) cc_final: 0.7803 (pt) REVERT: T 67 MET cc_start: 0.8193 (pp-130) cc_final: 0.7373 (tmm) REVERT: X 46 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5017 (mm) REVERT: X 53 ILE cc_start: 0.5247 (mt) cc_final: 0.5030 (mp) REVERT: X 169 ARG cc_start: 0.7113 (ttm170) cc_final: 0.6541 (ptm160) REVERT: X 180 ASN cc_start: 0.5601 (m-40) cc_final: 0.5378 (m-40) REVERT: X 194 LEU cc_start: 0.7989 (tt) cc_final: 0.7435 (tt) outliers start: 37 outliers final: 15 residues processed: 533 average time/residue: 0.1872 time to fit residues: 139.9514 Evaluate side-chains 402 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 383 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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: 6.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.6995 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9341 Z= 0.243 Angle : 0.845 10.597 12654 Z= 0.412 Chirality : 0.044 0.293 1558 Planarity : 0.006 0.056 1537 Dihedral : 6.657 54.586 1276 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.43 % Allowed : 5.60 % Favored : 93.97 % 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: -3.23 (0.21), residues: 1192 helix: -1.74 (0.15), residues: 950 sheet: None (None), residues: 0 loop : -2.99 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 234 HIS 0.007 0.002 HIS X 185 PHE 0.028 0.002 PHE Q 64 TYR 0.031 0.002 TYR X 241 ARG 0.003 0.000 ARG U 50 *********************** 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 476 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 472 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.7490 (mp) cc_final: 0.7252 (tp) REVERT: L 10 ILE cc_start: 0.8402 (mt) cc_final: 0.8109 (mt) REVERT: L 39 ARG cc_start: 0.7297 (ptm-80) cc_final: 0.6786 (tmt-80) REVERT: O 48 PHE cc_start: 0.7433 (t80) cc_final: 0.7232 (t80) REVERT: R 24 ILE cc_start: 0.9449 (mm) cc_final: 0.9001 (mt) REVERT: S 43 ILE cc_start: 0.7437 (tt) cc_final: 0.7149 (tt) REVERT: S 47 VAL cc_start: 0.9071 (t) cc_final: 0.8810 (p) REVERT: S 66 LEU cc_start: 0.8329 (pt) cc_final: 0.8089 (pt) REVERT: T 57 LEU cc_start: 0.7511 (mp) cc_final: 0.7164 (mt) REVERT: 8 17 PHE cc_start: 0.6938 (t80) cc_final: 0.6610 (t80) REVERT: 8 21 ILE cc_start: 0.7861 (mp) cc_final: 0.7606 (mm) REVERT: 8 37 ARG cc_start: 0.7543 (mtp180) cc_final: 0.6814 (mtp-110) REVERT: X 72 MET cc_start: 0.8394 (tmm) cc_final: 0.8067 (tmm) REVERT: X 185 HIS cc_start: 0.6808 (t70) cc_final: 0.6594 (t-90) REVERT: J 27 MET cc_start: 0.8258 (tpp) cc_final: 0.7954 (mmp) outliers start: 4 outliers final: 1 residues processed: 474 average time/residue: 0.1842 time to fit residues: 123.2199 Evaluate side-chains 384 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 383 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 62 GLN ** 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: 0.6990 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9341 Z= 0.227 Angle : 0.797 12.254 12654 Z= 0.382 Chirality : 0.044 0.263 1558 Planarity : 0.005 0.056 1537 Dihedral : 6.078 50.892 1276 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.11 % Allowed : 5.92 % Favored : 93.97 % 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: -2.04 (0.23), residues: 1192 helix: -0.90 (0.16), residues: 903 sheet: None (None), residues: 0 loop : -2.36 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 234 HIS 0.004 0.001 HIS X 185 PHE 0.027 0.002 PHE X 224 TYR 0.017 0.002 TYR X 44 ARG 0.004 0.001 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 461 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 460 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8130 (mt) cc_final: 0.7923 (mt) REVERT: L 39 ARG cc_start: 0.7225 (ptm-80) cc_final: 0.6711 (tmt-80) REVERT: L 66 LEU cc_start: 0.6649 (pt) cc_final: 0.6140 (mt) REVERT: O 15 SER cc_start: 0.7279 (p) cc_final: 0.6758 (m) REVERT: R 47 VAL cc_start: 0.8669 (t) cc_final: 0.8372 (p) REVERT: S 64 PHE cc_start: 0.7348 (m-10) cc_final: 0.7099 (m-10) REVERT: 8 25 ILE cc_start: 0.8975 (mt) cc_final: 0.8774 (mt) REVERT: X 71 ASN cc_start: 0.7545 (m-40) cc_final: 0.7226 (m-40) REVERT: U 73 ILE cc_start: 0.5456 (mt) cc_final: 0.5151 (mt) REVERT: U 76 PHE cc_start: 0.6595 (t80) cc_final: 0.6232 (m-80) REVERT: U 80 MET cc_start: 0.5294 (tpp) cc_final: 0.5080 (mtp) REVERT: J 27 MET cc_start: 0.8327 (tpp) cc_final: 0.8084 (mmp) outliers start: 1 outliers final: 0 residues processed: 461 average time/residue: 0.1894 time to fit residues: 124.6097 Evaluate side-chains 382 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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: 0.6980 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** 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: 0.7039 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9341 Z= 0.248 Angle : 0.790 12.027 12654 Z= 0.383 Chirality : 0.043 0.272 1558 Planarity : 0.005 0.057 1537 Dihedral : 5.899 50.391 1276 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 5.49 % 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: -1.77 (0.23), residues: 1192 helix: -0.71 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -2.41 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.048 0.002 PHE Q 64 TYR 0.024 0.002 TYR O 9 ARG 0.005 0.001 ARG P 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 454 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 0.945 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: L 39 ARG cc_start: 0.7189 (ptm-80) cc_final: 0.6704 (tmt-80) REVERT: L 66 LEU cc_start: 0.6729 (pt) cc_final: 0.6107 (mt) REVERT: P 24 ILE cc_start: 0.9180 (mt) cc_final: 0.8944 (mt) REVERT: P 67 MET cc_start: 0.7836 (ppp) cc_final: 0.7273 (ppp) REVERT: Q 61 THR cc_start: 0.8557 (p) cc_final: 0.8346 (p) REVERT: R 4 VAL cc_start: 0.8535 (m) cc_final: 0.8283 (p) REVERT: R 47 VAL cc_start: 0.8724 (t) cc_final: 0.8412 (p) REVERT: S 64 PHE cc_start: 0.7434 (m-10) cc_final: 0.7153 (m-10) REVERT: 8 25 ILE cc_start: 0.8995 (mt) cc_final: 0.8760 (mt) REVERT: X 105 ILE cc_start: 0.7914 (mt) cc_final: 0.7417 (mt) REVERT: X 221 MET cc_start: 0.8474 (mtt) cc_final: 0.7969 (mtt) REVERT: 7 157 LYS cc_start: 0.5570 (mtmt) cc_final: 0.4909 (tttm) REVERT: U 80 MET cc_start: 0.5281 (tpp) cc_final: 0.4970 (mtp) REVERT: J 27 MET cc_start: 0.8454 (tpp) cc_final: 0.8220 (mmp) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.1730 time to fit residues: 112.6382 Evaluate side-chains 377 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 230 GLN ** 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: 0.6988 moved from start: 0.5292 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= 0.226 Angle : 0.797 12.519 12654 Z= 0.377 Chirality : 0.043 0.222 1558 Planarity : 0.004 0.053 1537 Dihedral : 5.717 47.884 1276 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.22 % Allowed : 3.98 % Favored : 95.80 % 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: -1.27 (0.24), residues: 1192 helix: -0.42 (0.17), residues: 917 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 275 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 0.032 0.002 PHE X 224 TYR 0.026 0.001 TYR U 55 ARG 0.004 0.001 ARG Q 39 *********************** 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 451 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 449 time to evaluate : 0.996 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: L 39 ARG cc_start: 0.7135 (ptm-80) cc_final: 0.6692 (tmt-80) REVERT: L 66 LEU cc_start: 0.6671 (pt) cc_final: 0.6058 (mt) REVERT: P 67 MET cc_start: 0.7789 (ppp) cc_final: 0.7305 (ppp) REVERT: R 4 VAL cc_start: 0.8427 (m) cc_final: 0.8190 (p) REVERT: R 47 VAL cc_start: 0.8661 (t) cc_final: 0.8387 (p) REVERT: 8 10 MET cc_start: 0.5939 (mmp) cc_final: 0.5712 (mmp) REVERT: X 221 MET cc_start: 0.8496 (mtt) cc_final: 0.7941 (mtt) REVERT: 7 157 LYS cc_start: 0.5672 (mtmt) cc_final: 0.5291 (tttm) REVERT: 7 173 MET cc_start: 0.5673 (pmm) cc_final: 0.5441 (ptp) REVERT: U 80 MET cc_start: 0.5711 (tpp) cc_final: 0.5302 (mtp) REVERT: J 27 MET cc_start: 0.8272 (tpp) cc_final: 0.8048 (mmp) outliers start: 2 outliers final: 1 residues processed: 450 average time/residue: 0.1716 time to fit residues: 111.3863 Evaluate side-chains 375 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 5.9990 chunk 100 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** 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: 0.6968 moved from start: 0.5622 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= 0.213 Angle : 0.808 11.042 12654 Z= 0.380 Chirality : 0.043 0.228 1558 Planarity : 0.004 0.051 1537 Dihedral : 5.583 45.259 1276 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: -1.00 (0.24), residues: 1192 helix: -0.23 (0.17), residues: 901 sheet: None (None), residues: 0 loop : -1.67 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.027 0.002 PHE X 224 TYR 0.014 0.001 TYR 8 15 ARG 0.004 0.001 ARG Q 39 *********************** 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 443 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 1.043 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 50 MET cc_start: 0.6864 (ttp) cc_final: 0.6597 (ttp) REVERT: L 39 ARG cc_start: 0.7019 (ptm-80) cc_final: 0.6641 (tmt-80) REVERT: L 66 LEU cc_start: 0.6744 (pt) cc_final: 0.5935 (mt) REVERT: M 16 THR cc_start: 0.7845 (m) cc_final: 0.7606 (m) REVERT: M 19 LEU cc_start: 0.7189 (pt) cc_final: 0.6775 (pp) REVERT: M 67 MET cc_start: 0.6986 (ppp) cc_final: 0.6462 (ppp) REVERT: P 67 MET cc_start: 0.7689 (ppp) cc_final: 0.7166 (ppp) REVERT: R 4 VAL cc_start: 0.8512 (m) cc_final: 0.8295 (p) REVERT: R 47 VAL cc_start: 0.8509 (t) cc_final: 0.8274 (p) REVERT: R 59 GLU cc_start: 0.8148 (pt0) cc_final: 0.7861 (pt0) REVERT: S 57 LEU cc_start: 0.8531 (mt) cc_final: 0.8245 (mt) REVERT: 8 10 MET cc_start: 0.6173 (mmp) cc_final: 0.5958 (mmp) REVERT: X 221 MET cc_start: 0.8468 (mtt) cc_final: 0.7969 (mtt) REVERT: 7 157 LYS cc_start: 0.6041 (mtmt) cc_final: 0.5500 (tttm) REVERT: U 80 MET cc_start: 0.5616 (tpp) cc_final: 0.5274 (mtp) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.1740 time to fit residues: 110.8929 Evaluate side-chains 372 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6969 moved from start: 0.5881 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= 0.226 Angle : 0.820 12.949 12654 Z= 0.383 Chirality : 0.044 0.342 1558 Planarity : 0.004 0.049 1537 Dihedral : 5.441 43.543 1276 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -1.08 (0.24), residues: 1192 helix: -0.33 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 58 HIS 0.002 0.001 HIS X 137 PHE 0.022 0.002 PHE X 167 TYR 0.021 0.002 TYR M 9 ARG 0.002 0.000 ARG Z 84 *********************** 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 430 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 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: L 39 ARG cc_start: 0.6983 (ptm-80) cc_final: 0.6605 (tmt-80) REVERT: M 19 LEU cc_start: 0.7117 (pt) cc_final: 0.6701 (pp) REVERT: M 67 MET cc_start: 0.7049 (ppp) cc_final: 0.6671 (ppp) REVERT: P 67 MET cc_start: 0.7592 (ppp) cc_final: 0.7088 (ppp) REVERT: R 4 VAL cc_start: 0.8399 (m) cc_final: 0.8148 (p) REVERT: R 34 ILE cc_start: 0.9150 (mm) cc_final: 0.8933 (mm) REVERT: R 47 VAL cc_start: 0.8502 (t) cc_final: 0.8159 (p) REVERT: X 88 MET cc_start: 0.7702 (ttm) cc_final: 0.7374 (ttp) REVERT: X 221 MET cc_start: 0.8411 (mtt) cc_final: 0.7891 (mtt) REVERT: X 223 GLU cc_start: 0.8623 (pp20) cc_final: 0.8411 (pp20) REVERT: Z 71 LYS cc_start: 0.8447 (tmmt) cc_final: 0.8122 (mmtm) REVERT: 7 157 LYS cc_start: 0.5857 (mtmt) cc_final: 0.5424 (tttm) REVERT: 7 173 MET cc_start: 0.5542 (pmm) cc_final: 0.5261 (ptp) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.1659 time to fit residues: 103.3583 Evaluate side-chains 362 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 0.0000 chunk 107 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- 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 100 ASN X 114 HIS ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9341 Z= 0.238 Angle : 0.849 12.703 12654 Z= 0.398 Chirality : 0.046 0.313 1558 Planarity : 0.004 0.049 1537 Dihedral : 5.447 43.087 1276 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % 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: -1.08 (0.24), residues: 1192 helix: -0.32 (0.17), residues: 959 sheet: None (None), residues: 0 loop : -1.82 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.029 0.002 PHE 8 27 TYR 0.013 0.002 TYR X 66 ARG 0.001 0.000 ARG M 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 429 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 1.102 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: L 5 LEU cc_start: 0.7720 (mm) cc_final: 0.7295 (mm) REVERT: L 39 ARG cc_start: 0.6885 (ptm-80) cc_final: 0.6437 (tmt-80) REVERT: L 71 LEU cc_start: 0.8398 (pp) cc_final: 0.8183 (pp) REVERT: M 67 MET cc_start: 0.7083 (ppp) cc_final: 0.6773 (ppp) REVERT: N 10 ILE cc_start: 0.7625 (tp) cc_final: 0.7423 (tp) REVERT: P 67 MET cc_start: 0.7608 (ppp) cc_final: 0.7119 (ppp) REVERT: R 4 VAL cc_start: 0.8434 (m) cc_final: 0.8201 (p) REVERT: R 34 ILE cc_start: 0.9111 (mm) cc_final: 0.8869 (mm) REVERT: R 47 VAL cc_start: 0.8543 (t) cc_final: 0.8198 (p) REVERT: X 221 MET cc_start: 0.8437 (mtt) cc_final: 0.7918 (mtt) REVERT: Z 71 LYS cc_start: 0.8514 (tmmt) cc_final: 0.7732 (mmtm) REVERT: Z 86 LYS cc_start: 0.8140 (tptp) cc_final: 0.7921 (tptp) REVERT: 7 157 LYS cc_start: 0.6166 (mtmt) cc_final: 0.5749 (tttm) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1685 time to fit residues: 104.5887 Evaluate side-chains 366 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 0.0570 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9341 Z= 0.232 Angle : 0.839 12.375 12654 Z= 0.393 Chirality : 0.044 0.249 1558 Planarity : 0.004 0.046 1537 Dihedral : 5.345 41.482 1276 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.95 (0.24), residues: 1192 helix: -0.25 (0.17), residues: 958 sheet: None (None), residues: 0 loop : -1.69 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.025 0.002 PHE U 76 TYR 0.016 0.002 TYR M 9 ARG 0.001 0.000 ARG M 39 *********************** 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 435 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 1.051 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: L 5 LEU cc_start: 0.7767 (mm) cc_final: 0.7359 (mm) REVERT: L 39 ARG cc_start: 0.6877 (ptm-80) cc_final: 0.6439 (tmt-80) REVERT: M 9 TYR cc_start: 0.6709 (m-80) cc_final: 0.6143 (m-10) REVERT: M 19 LEU cc_start: 0.7107 (pt) cc_final: 0.6613 (pp) REVERT: M 67 MET cc_start: 0.7259 (ppp) cc_final: 0.6880 (ppp) REVERT: P 67 MET cc_start: 0.7560 (ppp) cc_final: 0.7144 (ppp) REVERT: X 88 MET cc_start: 0.7364 (ttm) cc_final: 0.7129 (ttm) REVERT: X 162 GLU cc_start: 0.7002 (tp30) cc_final: 0.6795 (tp30) REVERT: Z 71 LYS cc_start: 0.8396 (tmmt) cc_final: 0.7731 (mmtm) REVERT: 7 173 MET cc_start: 0.5114 (pmm) cc_final: 0.4676 (ptt) REVERT: U 73 ILE cc_start: 0.5048 (mm) cc_final: 0.4731 (mm) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1643 time to fit residues: 103.8466 Evaluate side-chains 376 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 0.0270 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.0270 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9341 Z= 0.222 Angle : 0.876 14.980 12654 Z= 0.400 Chirality : 0.045 0.221 1558 Planarity : 0.004 0.047 1537 Dihedral : 5.306 38.635 1276 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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: -0.93 (0.24), residues: 1192 helix: -0.21 (0.17), residues: 958 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 234 HIS 0.003 0.001 HIS X 185 PHE 0.028 0.002 PHE X 224 TYR 0.021 0.002 TYR X 232 ARG 0.001 0.000 ARG P 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 439 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 5 LEU cc_start: 0.7820 (mm) cc_final: 0.7370 (mm) REVERT: L 39 ARG cc_start: 0.6845 (ptm-80) cc_final: 0.6399 (tmt-80) REVERT: L 42 SER cc_start: 0.7738 (p) cc_final: 0.6837 (p) REVERT: L 73 LEU cc_start: 0.5888 (pp) cc_final: 0.5534 (mt) REVERT: M 9 TYR cc_start: 0.6423 (m-80) cc_final: 0.5902 (m-10) REVERT: M 16 THR cc_start: 0.7931 (m) cc_final: 0.7714 (m) REVERT: M 19 LEU cc_start: 0.7052 (pt) cc_final: 0.6664 (pp) REVERT: M 67 MET cc_start: 0.7189 (ppp) cc_final: 0.6596 (ppp) REVERT: N 50 MET cc_start: 0.4364 (mmp) cc_final: 0.4163 (mmp) REVERT: P 67 MET cc_start: 0.7398 (ppp) cc_final: 0.6983 (ppp) REVERT: S 47 VAL cc_start: 0.8571 (t) cc_final: 0.8322 (t) REVERT: S 66 LEU cc_start: 0.7688 (pt) cc_final: 0.7335 (pt) REVERT: 8 12 GLN cc_start: 0.7546 (tt0) cc_final: 0.6979 (tt0) REVERT: X 88 MET cc_start: 0.7230 (ttm) cc_final: 0.7001 (ttm) REVERT: X 176 ARG cc_start: 0.7436 (ttm110) cc_final: 0.7150 (ttm110) REVERT: X 221 MET cc_start: 0.8034 (mtp) cc_final: 0.7679 (mtp) REVERT: Z 71 LYS cc_start: 0.8482 (tmmt) cc_final: 0.7683 (mmtm) REVERT: 7 142 LYS cc_start: 0.7588 (tmtt) cc_final: 0.7251 (tptp) REVERT: U 73 ILE cc_start: 0.5012 (mm) cc_final: 0.4650 (mm) REVERT: J 9 ILE cc_start: 0.7590 (tp) cc_final: 0.7342 (mm) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1695 time to fit residues: 107.7333 Evaluate side-chains 392 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.132252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.112757 restraints weight = 25911.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.114564 restraints weight = 17887.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.115130 restraints weight = 12976.487| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9341 Z= 0.226 Angle : 0.860 15.610 12654 Z= 0.398 Chirality : 0.045 0.214 1558 Planarity : 0.004 0.047 1537 Dihedral : 5.250 37.288 1276 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % 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: -0.77 (0.24), residues: 1192 helix: -0.11 (0.17), residues: 958 sheet: None (None), residues: 0 loop : -1.70 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.031 0.002 PHE X 141 TYR 0.033 0.002 TYR K 9 ARG 0.001 0.000 ARG M 39 =============================================================================== Job complete usr+sys time: 2532.54 seconds wall clock time: 46 minutes 15.32 seconds (2775.32 seconds total)