Starting phenix.real_space_refine on Tue Feb 13 20:56:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/02_2024/6zik_11227_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/02_2024/6zik_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_11227/02_2024/6zik_11227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/02_2024/6zik_11227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/02_2024/6zik_11227_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zik_11227/02_2024/6zik_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.62, per 1000 atoms: 0.60 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 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: 1.71 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: 2.36 Time building geometry restraints manager: 3.46 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: 5.680 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: 0.020 Extract box with map and model: 26.020 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 25.780 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.090 ------------------------------------------------------------------------------- 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 : 0.854 Fit side-chains REVERT: G 8 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.5858 (tpt-90) REVERT: M 66 MET cc_start: 0.6191 (mmp) cc_final: 0.5792 (tmm) REVERT: Q 56 LEU cc_start: 0.8172 (tp) cc_final: 0.7935 (tp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1609 time to fit residues: 41.2633 Evaluate side-chains 144 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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: 0.6980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7647 moved from start: 0.0930 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= 0.261 Angle : 0.553 6.925 10600 Z= 0.288 Chirality : 0.040 0.146 1255 Planarity : 0.004 0.086 1324 Dihedral : 5.869 57.517 1130 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.60 % Allowed : 10.78 % Favored : 86.62 % 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: 1.36 (0.27), residues: 1002 helix: 1.53 (0.19), residues: 767 sheet: -0.91 (0.52), residues: 86 loop : -1.04 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP I 4 HIS 0.002 0.001 HIS G 66 PHE 0.021 0.002 PHE P 63 TYR 0.029 0.002 TYR G 171 ARG 0.005 0.001 ARG G 8 *********************** 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 186 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 0.903 Fit side-chains REVERT: G 8 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.5908 (ttt90) REVERT: H 91 GLN cc_start: 0.8523 (mp10) cc_final: 0.8149 (mt0) REVERT: H 132 GLN cc_start: 0.7011 (tm-30) cc_final: 0.6496 (tm-30) REVERT: L 60 MET cc_start: 0.6758 (mmt) cc_final: 0.6284 (mmt) REVERT: M 66 MET cc_start: 0.6161 (mmp) cc_final: 0.5825 (tmm) REVERT: Q 54 PHE cc_start: 0.8516 (t80) cc_final: 0.8275 (t80) outliers start: 20 outliers final: 16 residues processed: 176 average time/residue: 0.1685 time to fit residues: 42.1357 Evaluate side-chains 169 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 75 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7850 Z= 0.224 Angle : 0.527 6.883 10600 Z= 0.274 Chirality : 0.039 0.148 1255 Planarity : 0.004 0.071 1324 Dihedral : 5.666 57.067 1130 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.25 % Allowed : 15.71 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1002 helix: 1.72 (0.19), residues: 767 sheet: -0.93 (0.52), 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 0.011 0.002 HIS G 66 PHE 0.023 0.002 PHE P 54 TYR 0.025 0.001 TYR G 171 ARG 0.004 0.000 ARG G 8 *********************** 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 191 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 0.827 Fit side-chains REVERT: G 8 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.5814 (tpt-90) REVERT: H 91 GLN cc_start: 0.8484 (mp10) cc_final: 0.8188 (mt0) REVERT: L 60 MET cc_start: 0.6570 (mmp) cc_final: 0.6358 (mmt) REVERT: M 66 MET cc_start: 0.6119 (mmp) cc_final: 0.5816 (tmm) REVERT: P 54 PHE cc_start: 0.8618 (t80) cc_final: 0.8308 (t80) outliers start: 25 outliers final: 17 residues processed: 178 average time/residue: 0.1695 time to fit residues: 42.1390 Evaluate side-chains 170 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 33 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 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: 0.7641 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7850 Z= 0.235 Angle : 0.524 6.120 10600 Z= 0.274 Chirality : 0.039 0.186 1255 Planarity : 0.003 0.054 1324 Dihedral : 5.569 56.942 1130 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.51 % Allowed : 19.09 % Favored : 77.40 % 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: 1.63 (0.27), residues: 1002 helix: 1.77 (0.19), residues: 767 sheet: -1.05 (0.51), residues: 88 loop : -1.07 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.002 0.001 HIS G 120 PHE 0.019 0.002 PHE P 54 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 194 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 0.851 Fit side-chains REVERT: G 8 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.5946 (tpt-90) REVERT: H 91 GLN cc_start: 0.8562 (mp10) cc_final: 0.8326 (mt0) REVERT: M 66 MET cc_start: 0.6096 (mmp) cc_final: 0.5772 (tmm) REVERT: O 75 MET cc_start: 0.4663 (OUTLIER) cc_final: 0.4271 (tmm) outliers start: 27 outliers final: 18 residues processed: 182 average time/residue: 0.1766 time to fit residues: 45.7793 Evaluate side-chains 171 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 75 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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: 0.7595 moved from start: 0.1738 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= 0.170 Angle : 0.511 9.582 10600 Z= 0.258 Chirality : 0.038 0.174 1255 Planarity : 0.003 0.049 1324 Dihedral : 5.362 56.492 1130 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.99 % Allowed : 20.65 % Favored : 76.36 % 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: 1.93 (0.27), residues: 1002 helix: 1.97 (0.19), residues: 766 sheet: -0.81 (0.53), residues: 88 loop : -1.02 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.001 0.000 HIS G 120 PHE 0.026 0.001 PHE P 54 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 190 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 0.845 Fit side-chains REVERT: G 8 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.5882 (tpt-90) REVERT: G 205 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7489 (mm-40) REVERT: H 91 GLN cc_start: 0.8472 (mp10) cc_final: 0.8207 (mt0) REVERT: M 66 MET cc_start: 0.5991 (mmp) cc_final: 0.5771 (tmm) REVERT: Q 65 LEU cc_start: 0.8681 (tp) cc_final: 0.8427 (tp) REVERT: O 54 PHE cc_start: 0.8253 (t80) cc_final: 0.7989 (t80) REVERT: O 75 MET cc_start: 0.4673 (OUTLIER) cc_final: 0.4290 (tmm) outliers start: 23 outliers final: 16 residues processed: 181 average time/residue: 0.1741 time to fit residues: 44.0289 Evaluate side-chains 170 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 75 MET 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: 1.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.7710 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7850 Z= 0.398 Angle : 0.652 10.353 10600 Z= 0.332 Chirality : 0.044 0.292 1255 Planarity : 0.004 0.051 1324 Dihedral : 5.739 58.932 1130 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.45 % Allowed : 19.48 % Favored : 75.06 % 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: 1.23 (0.27), residues: 1002 helix: 1.48 (0.19), residues: 767 sheet: -1.34 (0.49), residues: 91 loop : -1.05 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 PHE 0.022 0.002 PHE M 8 TYR 0.031 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 209 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: G 8 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.6037 (tpt-90) REVERT: H 91 GLN cc_start: 0.8560 (mp10) cc_final: 0.8167 (mt0) REVERT: H 120 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6139 (pp) REVERT: I 11 TYR cc_start: 0.9082 (t80) cc_final: 0.8786 (t80) REVERT: M 66 MET cc_start: 0.6262 (mmp) cc_final: 0.5841 (tmm) REVERT: P 47 PHE cc_start: 0.8298 (t80) cc_final: 0.8094 (t80) REVERT: Q 56 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7852 (mp) REVERT: R 51 ILE cc_start: 0.8542 (mm) cc_final: 0.8248 (mt) REVERT: O 60 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7436 (tmm) REVERT: O 75 MET cc_start: 0.4768 (tmm) cc_final: 0.4403 (tmm) outliers start: 42 outliers final: 31 residues processed: 191 average time/residue: 0.1688 time to fit residues: 45.5388 Evaluate side-chains 193 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7850 Z= 0.196 Angle : 0.535 8.591 10600 Z= 0.273 Chirality : 0.039 0.166 1255 Planarity : 0.003 0.049 1324 Dihedral : 5.457 57.584 1130 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.16 % Allowed : 21.56 % Favored : 74.29 % 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: 1.69 (0.27), residues: 1002 helix: 1.81 (0.19), residues: 763 sheet: -0.93 (0.52), residues: 89 loop : -1.07 (0.51), residues: 150 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 0.016 0.001 PHE P 54 TYR 0.012 0.001 TYR G 171 ARG 0.002 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 200 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.110 Fit side-chains REVERT: G 8 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.5927 (tpt-90) REVERT: H 91 GLN cc_start: 0.8520 (mp10) cc_final: 0.8245 (mt0) REVERT: H 120 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5932 (pp) REVERT: M 66 MET cc_start: 0.6122 (mmp) cc_final: 0.5822 (tmm) REVERT: O 75 MET cc_start: 0.4597 (tmm) cc_final: 0.4242 (tmm) outliers start: 32 outliers final: 23 residues processed: 186 average time/residue: 0.1835 time to fit residues: 47.6873 Evaluate side-chains 186 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0060 chunk 18 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.2972 ------------------------------------------------------------------------------- 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: 0.7588 moved from start: 0.2111 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= 0.164 Angle : 0.524 8.108 10600 Z= 0.262 Chirality : 0.039 0.218 1255 Planarity : 0.003 0.049 1324 Dihedral : 5.216 57.096 1130 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.38 % Allowed : 22.86 % Favored : 73.77 % 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: 2.12 (0.27), residues: 1002 helix: 2.10 (0.19), residues: 761 sheet: -0.72 (0.53), residues: 90 loop : -0.82 (0.52), residues: 151 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 0.015 0.001 PHE P 63 TYR 0.030 0.001 TYR G 171 ARG 0.002 0.000 ARG I 23 *********************** 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 190 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 0.814 Fit side-chains REVERT: G 8 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.5891 (tpt-90) REVERT: G 18 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8079 (pttm) REVERT: G 78 CYS cc_start: 0.6275 (p) cc_final: 0.6021 (p) REVERT: H 91 GLN cc_start: 0.8506 (mp10) cc_final: 0.8206 (mt0) REVERT: H 120 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5911 (pp) REVERT: K 66 MET cc_start: 0.6016 (ppp) cc_final: 0.5801 (ppp) REVERT: O 75 MET cc_start: 0.4764 (tmm) cc_final: 0.4308 (tmm) outliers start: 26 outliers final: 23 residues processed: 179 average time/residue: 0.1690 time to fit residues: 42.7454 Evaluate side-chains 181 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 234 ASN H 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7850 Z= 0.247 Angle : 0.583 9.121 10600 Z= 0.289 Chirality : 0.040 0.239 1255 Planarity : 0.003 0.050 1324 Dihedral : 5.348 58.546 1130 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.16 % Allowed : 22.08 % Favored : 73.77 % 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: 1.91 (0.27), residues: 1002 helix: 1.95 (0.19), residues: 764 sheet: -0.80 (0.52), residues: 89 loop : -0.93 (0.53), residues: 149 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 0.019 0.002 PHE P 63 TYR 0.027 0.002 TYR G 171 ARG 0.003 0.000 ARG H 128 *********************** 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 194 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 0.829 Fit side-chains REVERT: G 8 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.5931 (tpt-90) REVERT: H 91 GLN cc_start: 0.8581 (mp10) cc_final: 0.8217 (mt0) REVERT: H 120 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5993 (pp) REVERT: I 26 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6507 (mp) REVERT: K 66 MET cc_start: 0.6036 (ppp) cc_final: 0.5790 (ppp) REVERT: O 75 MET cc_start: 0.4597 (tmm) cc_final: 0.4363 (tmm) outliers start: 32 outliers final: 26 residues processed: 180 average time/residue: 0.1713 time to fit residues: 43.5279 Evaluate side-chains 187 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.0030 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 0.0570 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7850 Z= 0.184 Angle : 0.559 8.577 10600 Z= 0.274 Chirality : 0.038 0.209 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.262 57.787 1130 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.38 % Allowed : 22.47 % Favored : 74.16 % 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: 2.10 (0.27), residues: 1002 helix: 2.14 (0.19), residues: 750 sheet: -0.72 (0.53), residues: 90 loop : -0.90 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.001 0.001 HIS H 66 PHE 0.016 0.001 PHE P 63 TYR 0.026 0.001 TYR G 171 ARG 0.003 0.000 ARG I 23 ********************** 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 189 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 0.821 Fit side-chains REVERT: G 8 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.5943 (tpt-90) REVERT: H 91 GLN cc_start: 0.8530 (mp10) cc_final: 0.8270 (mt0) REVERT: H 120 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.5926 (pp) REVERT: I 26 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6550 (mp) REVERT: O 75 MET cc_start: 0.4626 (tmm) cc_final: 0.4404 (tmm) outliers start: 26 outliers final: 23 residues processed: 179 average time/residue: 0.1713 time to fit residues: 42.8700 Evaluate side-chains 183 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.138236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114946 restraints weight = 11020.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117777 restraints weight = 6624.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119515 restraints weight = 4765.618| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7850 Z= 0.251 Angle : 0.591 8.907 10600 Z= 0.293 Chirality : 0.041 0.234 1255 Planarity : 0.003 0.049 1324 Dihedral : 5.364 58.735 1130 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.64 % Allowed : 22.86 % Favored : 73.51 % 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: 1.86 (0.27), residues: 1002 helix: 1.94 (0.19), residues: 764 sheet: -0.95 (0.51), residues: 91 loop : -1.02 (0.52), 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 51 PHE 0.021 0.002 PHE P 54 TYR 0.026 0.002 TYR G 171 ARG 0.002 0.000 ARG I 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1988.62 seconds wall clock time: 37 minutes 11.27 seconds (2231.27 seconds total)