Starting phenix.real_space_refine on Fri Dec 8 07:53:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/12_2023/6zik_11227_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/12_2023/6zik_11227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/12_2023/6zik_11227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/12_2023/6zik_11227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/12_2023/6zik_11227_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/12_2023/6zik_11227_updated.pdb" } resolution = 3.66 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.002 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 41 5.16 5 C 5014 2.51 5 N 1260 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 9": "NH1" <-> "NH2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ARG 202": "NH1" <-> "NH2" Residue "G TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 206": "OE1" <-> "OE2" Residue "G GLU 224": "OE1" <-> "OE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7735 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2115 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 979 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 369 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 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} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 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} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.58, per 1000 atoms: 0.72 Number of scatterers: 7735 At special positions: 0 Unit cell: (70.216, 68.12, 188.64, 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 41 16.00 O 1420 8.00 N 1260 7.00 C 5014 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: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 3 sheets defined 72.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'G' and resid 3 through 54 removed outlier: 3.667A pdb=" N ARG G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 4.212A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 117 through 123 removed outlier: 3.688A pdb=" N SER G 121 " --> pdb=" O HIS G 117 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASP G 122 " --> pdb=" O ARG G 118 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN G 123 " --> pdb=" O THR G 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 123' Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 200 through 271 removed outlier: 3.808A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 117 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 11 through 25 removed outlier: 4.099A pdb=" N ALA I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 35 removed outlier: 3.633A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 38 removed outlier: 4.318A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLY K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY K 20 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 72 removed outlier: 4.237A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 38 removed outlier: 3.892A pdb=" N VAL L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLY L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLY L 20 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 72 removed outlier: 3.624A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 3.973A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 72 removed outlier: 4.251A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 38 removed outlier: 4.077A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 72 removed outlier: 3.734A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 38 removed outlier: 4.472A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 73 removed outlier: 3.785A pdb=" N GLY P 61 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 38 removed outlier: 3.575A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 73 removed outlier: 3.604A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 38 removed outlier: 3.519A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 72 removed outlier: 4.111A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 4.177A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 72 removed outlier: 3.605A pdb=" N LEU O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.089A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR G 127 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 80 through 84 removed outlier: 6.045A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.667A pdb=" N GLN H 35 " --> pdb=" O HIS H 66 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1806 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: 2.48 Time building geometry restraints manager: 3.61 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: 2449 1.34 - 1.46: 1363 1.46 - 1.58: 3966 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 7850 Sorted by residual: bond pdb=" CB MET K 60 " pdb=" CG MET K 60 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CG1 ILE H 135 " pdb=" CD1 ILE H 135 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 bond pdb=" CG MET K 60 " pdb=" SD MET K 60 " ideal model delta sigma weight residual 1.803 1.769 0.034 2.50e-02 1.60e+03 1.86e+00 bond pdb=" CA GLY H 80 " pdb=" C GLY H 80 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.20e-02 6.94e+03 1.67e+00 bond pdb=" CB VAL K 16 " pdb=" CG1 VAL K 16 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 ... (remaining 7845 not shown) Histogram of bond angle deviations from ideal: 93.97 - 101.95: 29 101.95 - 109.92: 794 109.92 - 117.90: 5061 117.90 - 125.88: 4689 125.88 - 133.85: 27 Bond angle restraints: 10600 Sorted by residual: angle pdb=" CB MET K 60 " pdb=" CG MET K 60 " pdb=" SD MET K 60 " ideal model delta sigma weight residual 112.70 123.20 -10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CG MET K 60 " pdb=" SD MET K 60 " pdb=" CE MET K 60 " ideal model delta sigma weight residual 100.90 93.97 6.93 2.20e+00 2.07e-01 9.91e+00 angle pdb=" CA LYS H 114 " pdb=" CB LYS H 114 " pdb=" CG LYS H 114 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 angle pdb=" N GLN K 44 " pdb=" CA GLN K 44 " pdb=" C GLN K 44 " ideal model delta sigma weight residual 111.00 102.79 8.21 2.80e+00 1.28e-01 8.60e+00 angle pdb=" C SER H 117 " pdb=" N GLU H 118 " pdb=" CA GLU H 118 " ideal model delta sigma weight residual 122.65 118.04 4.61 1.60e+00 3.91e-01 8.31e+00 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4156 17.95 - 35.90: 373 35.90 - 53.85: 58 53.85 - 71.80: 9 71.80 - 89.75: 7 Dihedral angle restraints: 4603 sinusoidal: 1660 harmonic: 2943 Sorted by residual: dihedral pdb=" CA GLY G 79 " pdb=" C GLY G 79 " pdb=" N ALA G 80 " pdb=" CA ALA G 80 " ideal model delta harmonic sigma weight residual -180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA LEU Q 56 " pdb=" C LEU Q 56 " pdb=" N SER Q 57 " pdb=" CA SER Q 57 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE Q 73 " pdb=" C PHE Q 73 " pdb=" N ALA Q 74 " pdb=" CA ALA Q 74 " ideal model delta harmonic sigma weight residual -180.00 -162.16 -17.84 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 712 0.030 - 0.061: 354 0.061 - 0.091: 127 0.091 - 0.121: 54 0.121 - 0.152: 8 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA M3L R 43 " pdb=" N M3L R 43 " pdb=" C M3L R 43 " pdb=" CB M3L R 43 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE G 178 " pdb=" N ILE G 178 " pdb=" C ILE G 178 " pdb=" CB ILE G 178 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA M3L P 43 " pdb=" N M3L P 43 " pdb=" C M3L P 43 " pdb=" CB M3L P 43 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 1252 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 59 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO G 60 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 44 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLN K 44 " -0.067 2.00e-02 2.50e+03 pdb=" O GLN K 44 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN K 45 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 52 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO H 53 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " -0.027 5.00e-02 4.00e+02 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 134 2.69 - 3.24: 8276 3.24 - 3.79: 12908 3.79 - 4.35: 16262 4.35 - 4.90: 27438 Nonbonded interactions: 65018 Sorted by model distance: nonbonded pdb=" OG1 THR M 4 " pdb=" OD1 ASP N 3 " model vdw 2.134 2.440 nonbonded pdb=" OG SER P 21 " pdb=" O SER P 57 " model vdw 2.159 2.440 nonbonded pdb=" OG SER M 21 " pdb=" O SER M 57 " model vdw 2.170 2.440 nonbonded pdb=" OD1 ASN G 15 " pdb=" NZ LYS G 18 " model vdw 2.179 2.520 nonbonded pdb=" OG1 THR K 4 " pdb=" OD1 ASP L 3 " model vdw 2.207 2.440 ... (remaining 65013 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' selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = chain 'P' selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 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: 4.720 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: 24.990 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 27.890 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.005 0.056 7850 Z= 0.331 Angle : 0.729 10.502 10600 Z= 0.386 Chirality : 0.044 0.152 1255 Planarity : 0.005 0.117 1324 Dihedral : 14.227 89.754 2727 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 1002 helix: 1.35 (0.19), residues: 763 sheet: -1.09 (0.50), residues: 90 loop : -1.13 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.007 0.001 HIS G 66 PHE 0.021 0.002 PHE P 63 TYR 0.013 0.002 TYR G 193 ARG 0.010 0.001 ARG G 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.859 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1738 time to fit residues: 43.7742 Evaluate side-chains 144 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7850 Z= 0.281 Angle : 0.569 7.125 10600 Z= 0.296 Chirality : 0.040 0.147 1255 Planarity : 0.004 0.087 1324 Dihedral : 5.918 57.445 1130 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.60 % Allowed : 10.91 % Favored : 86.49 % 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: 1.26 (0.27), residues: 1002 helix: 1.47 (0.19), residues: 767 sheet: -1.05 (0.52), residues: 88 loop : -1.04 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 PHE 0.021 0.002 PHE P 63 TYR 0.029 0.002 TYR G 171 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 0.877 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 175 average time/residue: 0.1679 time to fit residues: 41.6312 Evaluate side-chains 167 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0782 time to fit residues: 3.3601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7850 Z= 0.271 Angle : 0.561 6.814 10600 Z= 0.290 Chirality : 0.040 0.155 1255 Planarity : 0.004 0.072 1324 Dihedral : 5.764 57.371 1130 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.56 % Allowed : 17.01 % Favored : 81.43 % 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: 1.37 (0.27), residues: 1002 helix: 1.57 (0.19), residues: 767 sheet: -1.16 (0.50), residues: 88 loop : -1.09 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.004 0.001 HIS G 120 PHE 0.025 0.002 PHE P 54 TYR 0.026 0.002 TYR G 171 ARG 0.002 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 0.867 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 172 average time/residue: 0.1873 time to fit residues: 44.8467 Evaluate side-chains 158 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0708 time to fit residues: 1.7733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7850 Z= 0.249 Angle : 0.538 6.561 10600 Z= 0.280 Chirality : 0.040 0.182 1255 Planarity : 0.004 0.062 1324 Dihedral : 5.622 56.855 1130 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.47 % Allowed : 19.35 % Favored : 78.18 % 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: 1.50 (0.27), residues: 1002 helix: 1.68 (0.19), residues: 767 sheet: -1.09 (0.51), residues: 89 loop : -1.17 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 120 PHE 0.019 0.002 PHE M 8 TYR 0.025 0.001 TYR G 171 ARG 0.004 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 0.886 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 180 average time/residue: 0.1698 time to fit residues: 43.8351 Evaluate side-chains 164 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0755 time to fit residues: 2.9887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7850 Z= 0.271 Angle : 0.572 7.941 10600 Z= 0.291 Chirality : 0.040 0.158 1255 Planarity : 0.004 0.055 1324 Dihedral : 5.627 56.931 1130 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.34 % Allowed : 19.87 % Favored : 77.79 % 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: 1.41 (0.27), residues: 1002 helix: 1.62 (0.19), residues: 767 sheet: -1.19 (0.50), residues: 88 loop : -1.11 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 PHE 0.030 0.002 PHE M 8 TYR 0.014 0.001 TYR G 171 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 174 average time/residue: 0.1573 time to fit residues: 39.0540 Evaluate side-chains 164 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0758 time to fit residues: 2.1133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7850 Z= 0.313 Angle : 0.601 8.548 10600 Z= 0.307 Chirality : 0.041 0.174 1255 Planarity : 0.004 0.052 1324 Dihedral : 5.685 56.689 1130 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.56 % Allowed : 22.34 % Favored : 76.10 % 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: 1.24 (0.27), residues: 1002 helix: 1.50 (0.19), residues: 767 sheet: -1.41 (0.49), residues: 91 loop : -1.07 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 PHE 0.023 0.002 PHE M 8 TYR 0.029 0.002 TYR G 171 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 0.923 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 172 average time/residue: 0.1635 time to fit residues: 39.9248 Evaluate side-chains 162 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0705 time to fit residues: 2.0770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7850 Z= 0.227 Angle : 0.555 8.451 10600 Z= 0.282 Chirality : 0.040 0.237 1255 Planarity : 0.003 0.051 1324 Dihedral : 5.542 56.815 1130 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.56 % Allowed : 23.64 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1002 helix: 1.65 (0.19), residues: 767 sheet: -1.06 (0.51), residues: 89 loop : -1.09 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 66 PHE 0.017 0.001 PHE P 63 TYR 0.013 0.001 TYR G 171 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 177 average time/residue: 0.1788 time to fit residues: 44.5576 Evaluate side-chains 167 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0749 time to fit residues: 2.1184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7850 Z= 0.239 Angle : 0.570 9.033 10600 Z= 0.287 Chirality : 0.040 0.192 1255 Planarity : 0.003 0.059 1324 Dihedral : 5.525 56.708 1130 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.56 % Allowed : 22.60 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 1002 helix: 1.67 (0.19), residues: 767 sheet: -1.12 (0.51), residues: 88 loop : -1.02 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 66 PHE 0.018 0.001 PHE P 63 TYR 0.013 0.001 TYR G 171 ARG 0.001 0.000 ARG K 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 0.790 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 170 average time/residue: 0.1605 time to fit residues: 38.5567 Evaluate side-chains 170 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0716 time to fit residues: 2.4700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 27 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7850 Z= 0.197 Angle : 0.559 8.649 10600 Z= 0.280 Chirality : 0.039 0.202 1255 Planarity : 0.003 0.058 1324 Dihedral : 5.413 57.213 1130 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.39 % Allowed : 24.03 % Favored : 75.58 % 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: 1.71 (0.27), residues: 1002 helix: 1.89 (0.19), residues: 754 sheet: -1.01 (0.53), residues: 89 loop : -1.18 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 4 HIS 0.001 0.000 HIS H 66 PHE 0.017 0.001 PHE P 63 TYR 0.014 0.001 TYR G 171 ARG 0.001 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 0.845 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 174 average time/residue: 0.1878 time to fit residues: 45.4830 Evaluate side-chains 160 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7850 Z= 0.258 Angle : 0.602 9.382 10600 Z= 0.300 Chirality : 0.041 0.237 1255 Planarity : 0.004 0.057 1324 Dihedral : 5.514 57.529 1130 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.65 % Allowed : 24.55 % Favored : 74.81 % 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: 1.66 (0.27), residues: 1002 helix: 1.74 (0.19), residues: 772 sheet: -1.18 (0.51), residues: 88 loop : -0.75 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 PHE 0.019 0.002 PHE P 63 TYR 0.017 0.002 TYR G 171 ARG 0.001 0.000 ARG G 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 0.771 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 161 average time/residue: 0.1762 time to fit residues: 39.8614 Evaluate side-chains 163 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0773 time to fit residues: 1.8154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0370 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116916 restraints weight = 10947.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119869 restraints weight = 6553.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121726 restraints weight = 4684.754| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7850 Z= 0.190 Angle : 0.561 9.237 10600 Z= 0.279 Chirality : 0.039 0.205 1255 Planarity : 0.004 0.058 1324 Dihedral : 5.369 57.199 1130 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.13 % Allowed : 24.68 % Favored : 75.19 % 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: 1.92 (0.28), residues: 1002 helix: 1.98 (0.19), residues: 764 sheet: -0.98 (0.53), residues: 89 loop : -0.93 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.001 0.000 HIS H 66 PHE 0.016 0.001 PHE P 63 TYR 0.017 0.001 TYR G 171 ARG 0.002 0.000 ARG N 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2011.99 seconds wall clock time: 41 minutes 11.99 seconds (2471.99 seconds total)