Starting phenix.real_space_refine on Sat Mar 16 20:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg8_11196/03_2024/6zg8_11196_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg8_11196/03_2024/6zg8_11196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg8_11196/03_2024/6zg8_11196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg8_11196/03_2024/6zg8_11196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg8_11196/03_2024/6zg8_11196_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg8_11196/03_2024/6zg8_11196_trim_updated.pdb" } resolution = 3.49 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: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 4996 2.51 5 N 1257 2.21 5 O 1417 1.98 5 H 7815 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ASP 182": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 1": "OD1" <-> "OD2" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 3": "OD1" <-> "OD2" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ASP 1": "OD1" <-> "OD2" Residue "O PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 1": "OD1" <-> "OD2" Residue "P ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15522 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1961 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} 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: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} 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: "M" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} 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: "N" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} 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: "O" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} 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: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} 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: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} 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: "R" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} 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 Time building chain proxies: 7.03, per 1000 atoms: 0.45 Number of scatterers: 15522 At special positions: 0 Unit cell: (67.072, 74.408, 187.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 O 1417 8.00 N 1257 7.00 C 4996 6.00 H 7815 1.00 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: 13.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 3 sheets defined 72.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'G' and resid 3 through 54 removed outlier: 3.643A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.607A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 99 removed outlier: 3.769A pdb=" N ALA G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 200 through 271 removed outlier: 3.548A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 248 " --> pdb=" O ASP G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 120 removed outlier: 4.201A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 11 through 25 Processing helix chain 'I' and resid 30 through 37 removed outlier: 3.655A pdb=" N THR I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 16 removed outlier: 4.343A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 38 removed outlier: 3.677A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 72 removed outlier: 3.732A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 16 removed outlier: 3.788A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 38 Processing helix chain 'L' and resid 45 through 73 removed outlier: 3.748A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 38 removed outlier: 4.035A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 73 removed outlier: 3.991A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY M 61 " --> pdb=" O SER M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 37 removed outlier: 3.936A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 72 removed outlier: 4.340A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 39 removed outlier: 3.710A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 72 removed outlier: 4.732A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY O 61 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 38 removed outlier: 3.993A pdb=" N PHE P 8 " --> pdb=" O THR P 4 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 73 removed outlier: 4.989A pdb=" N MET P 60 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY P 61 " --> pdb=" O SER P 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 38 removed outlier: 3.647A pdb=" N THR Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.813A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY Q 61 " --> pdb=" O SER Q 57 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 38 removed outlier: 3.984A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 73 removed outlier: 5.443A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY R 61 " --> pdb=" O SER R 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.300A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU G 102 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE G 68 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS G 104 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY G 70 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 106 " --> pdb=" O GLY G 70 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR G 127 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.512A pdb=" N ALA H 94 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 44 through 47 removed outlier: 6.933A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1779 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: 5.77 Time building geometry restraints manager: 13.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7805 1.03 - 1.23: 42 1.23 - 1.42: 3159 1.42 - 1.62: 4567 1.62 - 1.81: 64 Bond restraints: 15637 Sorted by residual: bond pdb=" CA VAL G 126 " pdb=" CB VAL G 126 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.89e+00 bond pdb=" CG1 ILE R 9 " pdb=" CD1 ILE R 9 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.32e+00 bond pdb=" CG1 ILE K 9 " pdb=" CD1 ILE K 9 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 bond pdb=" CB ILE K 9 " pdb=" CG2 ILE K 9 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.13e+00 bond pdb=" CB GLU R 58 " pdb=" CG GLU R 58 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.66e+00 ... (remaining 15632 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.96: 91 105.96 - 112.96: 18554 112.96 - 119.97: 4429 119.97 - 126.97: 5127 126.97 - 133.98: 26 Bond angle restraints: 28227 Sorted by residual: angle pdb=" N THR H 40 " pdb=" CA THR H 40 " pdb=" C THR H 40 " ideal model delta sigma weight residual 111.71 116.82 -5.11 1.34e+00 5.57e-01 1.46e+01 angle pdb=" C GLY L 53 " pdb=" N PHE L 54 " pdb=" CA PHE L 54 " ideal model delta sigma weight residual 120.31 115.33 4.98 1.52e+00 4.33e-01 1.07e+01 angle pdb=" N ILE G 169 " pdb=" CA ILE G 169 " pdb=" C ILE G 169 " ideal model delta sigma weight residual 112.96 109.81 3.15 1.00e+00 1.00e+00 9.89e+00 angle pdb=" N PHE L 54 " pdb=" CA PHE L 54 " pdb=" CB PHE L 54 " ideal model delta sigma weight residual 110.28 114.74 -4.46 1.55e+00 4.16e-01 8.27e+00 angle pdb=" N GLU K 58 " pdb=" CA GLU K 58 " pdb=" CB GLU K 58 " ideal model delta sigma weight residual 110.22 114.51 -4.29 1.54e+00 4.22e-01 7.76e+00 ... (remaining 28222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6453 17.90 - 35.81: 554 35.81 - 53.71: 231 53.71 - 71.61: 72 71.61 - 89.51: 10 Dihedral angle restraints: 7320 sinusoidal: 3889 harmonic: 3431 Sorted by residual: dihedral pdb=" CA LEU R 56 " pdb=" C LEU R 56 " pdb=" N SER R 57 " pdb=" CA SER R 57 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE I 44 " pdb=" C ILE I 44 " pdb=" N VAL I 45 " pdb=" CA VAL I 45 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA H 21 " pdb=" C ALA H 21 " pdb=" N SER H 22 " pdb=" CA SER H 22 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 7317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 824 0.035 - 0.070: 313 0.070 - 0.105: 72 0.105 - 0.140: 38 0.140 - 0.175: 4 Chirality restraints: 1251 Sorted by residual: chirality pdb=" CG LEU R 56 " pdb=" CB LEU R 56 " pdb=" CD1 LEU R 56 " pdb=" CD2 LEU R 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA MET K 60 " pdb=" N MET K 60 " pdb=" C MET K 60 " pdb=" CB MET K 60 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA M3L M 43 " pdb=" N M3L M 43 " pdb=" C M3L M 43 " pdb=" CB M3L M 43 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1248 not shown) Planarity restraints: 2329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 52 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C LEU L 52 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU L 52 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY L 53 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 54 " -0.013 2.00e-02 2.50e+03 1.04e-02 3.22e+00 pdb=" CG PHE K 54 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE K 54 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE K 54 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE K 54 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE K 54 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE K 54 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE K 54 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE K 54 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE K 54 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE K 54 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE K 54 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 66 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C MET L 66 " -0.030 2.00e-02 2.50e+03 pdb=" O MET L 66 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL L 67 " 0.010 2.00e-02 2.50e+03 ... (remaining 2326 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1671 2.23 - 2.82: 34992 2.82 - 3.41: 43886 3.41 - 4.01: 58100 4.01 - 4.60: 90572 Nonbonded interactions: 229221 Sorted by model distance: nonbonded pdb=" OD1 ASP G 74 " pdb=" H ASP G 110 " model vdw 1.637 1.850 nonbonded pdb=" OE1 GLN L 45 " pdb=" H GLN L 45 " model vdw 1.644 1.850 nonbonded pdb=" OD1 ASP Q 3 " pdb=" H THR Q 4 " model vdw 1.660 1.850 nonbonded pdb=" O SER G 180 " pdb=" H THR G 183 " model vdw 1.675 1.850 nonbonded pdb=" HG1 THR G 137 " pdb=" O GLY I 39 " model vdw 1.684 1.850 ... (remaining 229216 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' and resid 1 through 74) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 individual isotropic 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: 5.580 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: 0.260 Extract box with map and model: 27.040 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 54.680 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.006 0.081 7822 Z= 0.376 Angle : 0.687 8.530 10565 Z= 0.383 Chirality : 0.042 0.175 1251 Planarity : 0.004 0.039 1321 Dihedral : 14.972 89.513 2712 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 0.37 (0.27), residues: 999 helix: 0.95 (0.19), residues: 736 sheet: -0.79 (0.61), residues: 77 loop : -1.94 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.004 0.001 HIS G 82 PHE 0.028 0.002 PHE K 54 TYR 0.016 0.002 TYR G 44 ARG 0.013 0.001 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 41 THR cc_start: 0.8295 (p) cc_final: 0.7961 (m) REVERT: Q 70 LEU cc_start: 0.8055 (mt) cc_final: 0.7835 (mt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3873 time to fit residues: 85.1874 Evaluate side-chains 133 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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: 0.9990 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 255 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7822 Z= 0.210 Angle : 0.523 5.520 10565 Z= 0.284 Chirality : 0.038 0.137 1251 Planarity : 0.003 0.031 1321 Dihedral : 6.663 57.711 1127 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.78 % Allowed : 6.92 % Favored : 92.30 % 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: 1.13 (0.27), residues: 999 helix: 1.45 (0.19), residues: 761 sheet: -0.76 (0.57), residues: 89 loop : -1.72 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.003 0.001 HIS G 82 PHE 0.031 0.002 PHE L 54 TYR 0.010 0.001 TYR G 44 ARG 0.004 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 41 THR cc_start: 0.8330 (p) cc_final: 0.7963 (m) REVERT: K 15 THR cc_start: 0.8874 (t) cc_final: 0.8631 (m) REVERT: Q 70 LEU cc_start: 0.8015 (mt) cc_final: 0.7808 (mt) outliers start: 6 outliers final: 4 residues processed: 149 average time/residue: 0.3911 time to fit residues: 81.2081 Evaluate side-chains 146 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain Q residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7822 Z= 0.232 Angle : 0.508 6.415 10565 Z= 0.277 Chirality : 0.037 0.137 1251 Planarity : 0.003 0.031 1321 Dihedral : 6.685 57.491 1127 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.04 % Allowed : 10.57 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 999 helix: 1.70 (0.19), residues: 761 sheet: -0.73 (0.57), residues: 89 loop : -1.79 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.003 0.001 HIS G 82 PHE 0.022 0.001 PHE P 54 TYR 0.011 0.001 TYR G 171 ARG 0.004 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 41 THR cc_start: 0.8335 (p) cc_final: 0.7957 (m) REVERT: K 15 THR cc_start: 0.8901 (t) cc_final: 0.8662 (m) REVERT: Q 54 PHE cc_start: 0.7570 (t80) cc_final: 0.7363 (t80) outliers start: 8 outliers final: 7 residues processed: 146 average time/residue: 0.3651 time to fit residues: 75.5358 Evaluate side-chains 144 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain Q residue 46 LEU 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: 0.9980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7822 Z= 0.212 Angle : 0.496 5.158 10565 Z= 0.269 Chirality : 0.037 0.136 1251 Planarity : 0.003 0.030 1321 Dihedral : 6.527 53.485 1127 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.31 % Allowed : 12.14 % Favored : 86.55 % 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: 1.72 (0.27), residues: 999 helix: 1.92 (0.19), residues: 754 sheet: -0.73 (0.56), residues: 89 loop : -1.60 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 PHE 0.021 0.001 PHE P 54 TYR 0.010 0.001 TYR G 171 ARG 0.005 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 41 THR cc_start: 0.8332 (p) cc_final: 0.7951 (m) REVERT: K 15 THR cc_start: 0.8881 (t) cc_final: 0.8639 (m) REVERT: P 54 PHE cc_start: 0.8263 (t80) cc_final: 0.7992 (t80) outliers start: 10 outliers final: 8 residues processed: 148 average time/residue: 0.3441 time to fit residues: 73.1409 Evaluate side-chains 144 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7822 Z= 0.244 Angle : 0.514 5.862 10565 Z= 0.278 Chirality : 0.037 0.139 1251 Planarity : 0.003 0.032 1321 Dihedral : 6.623 57.726 1127 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.70 % Allowed : 13.58 % Favored : 84.73 % 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: 1.74 (0.27), residues: 999 helix: 1.95 (0.19), residues: 754 sheet: -0.69 (0.56), residues: 89 loop : -1.66 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.003 0.001 HIS G 82 PHE 0.015 0.002 PHE P 54 TYR 0.010 0.001 TYR G 171 ARG 0.006 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 15 THR cc_start: 0.8919 (t) cc_final: 0.8673 (m) REVERT: K 60 MET cc_start: 0.6996 (mmm) cc_final: 0.6558 (mmp) REVERT: P 54 PHE cc_start: 0.8316 (t80) cc_final: 0.8096 (t80) outliers start: 13 outliers final: 12 residues processed: 146 average time/residue: 0.3524 time to fit residues: 73.5080 Evaluate side-chains 148 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 15 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7822 Z= 0.220 Angle : 0.504 6.229 10565 Z= 0.271 Chirality : 0.037 0.137 1251 Planarity : 0.003 0.030 1321 Dihedral : 6.617 57.847 1127 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.31 % Allowed : 14.23 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.27), residues: 999 helix: 2.03 (0.19), residues: 754 sheet: -0.66 (0.56), residues: 89 loop : -1.59 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 PHE 0.015 0.001 PHE P 54 TYR 0.011 0.001 TYR G 171 ARG 0.005 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 15 THR cc_start: 0.8906 (t) cc_final: 0.8671 (m) REVERT: K 60 MET cc_start: 0.6907 (mmm) cc_final: 0.6569 (mmp) REVERT: P 54 PHE cc_start: 0.8324 (t80) cc_final: 0.8114 (t80) outliers start: 10 outliers final: 9 residues processed: 145 average time/residue: 0.3574 time to fit residues: 74.4461 Evaluate side-chains 146 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 9 ILE 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: 1.9990 chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7822 Z= 0.230 Angle : 0.509 6.420 10565 Z= 0.273 Chirality : 0.037 0.138 1251 Planarity : 0.003 0.039 1321 Dihedral : 6.602 56.813 1127 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.83 % Allowed : 14.88 % Favored : 83.29 % 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: 1.90 (0.27), residues: 999 helix: 2.06 (0.19), residues: 754 sheet: -0.64 (0.56), residues: 91 loop : -1.58 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 PHE 0.014 0.002 PHE H 45 TYR 0.011 0.001 TYR G 44 ARG 0.007 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: K 60 MET cc_start: 0.6788 (mmm) cc_final: 0.6165 (mmp) REVERT: L 4 THR cc_start: 0.7990 (p) cc_final: 0.7757 (m) outliers start: 14 outliers final: 10 residues processed: 149 average time/residue: 0.3429 time to fit residues: 73.6991 Evaluate side-chains 148 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 15 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 89 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: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7822 Z= 0.244 Angle : 0.519 6.739 10565 Z= 0.278 Chirality : 0.038 0.172 1251 Planarity : 0.003 0.042 1321 Dihedral : 6.638 58.284 1127 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.57 % Allowed : 14.75 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.27), residues: 999 helix: 2.03 (0.19), residues: 754 sheet: -0.62 (0.56), residues: 91 loop : -1.55 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 PHE 0.015 0.002 PHE H 45 TYR 0.012 0.001 TYR G 44 ARG 0.008 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: K 60 MET cc_start: 0.6699 (mmm) cc_final: 0.6404 (mmt) REVERT: L 4 THR cc_start: 0.8006 (p) cc_final: 0.7772 (m) outliers start: 12 outliers final: 10 residues processed: 147 average time/residue: 0.3473 time to fit residues: 73.7701 Evaluate side-chains 148 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain R residue 15 THR 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: 0.9980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7822 Z= 0.243 Angle : 0.520 7.061 10565 Z= 0.279 Chirality : 0.038 0.188 1251 Planarity : 0.003 0.046 1321 Dihedral : 6.603 51.573 1127 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.70 % Allowed : 15.01 % Favored : 83.29 % 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: 1.87 (0.27), residues: 999 helix: 2.03 (0.19), residues: 754 sheet: -0.63 (0.56), residues: 91 loop : -1.55 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 PHE 0.014 0.002 PHE K 54 TYR 0.012 0.001 TYR G 44 ARG 0.007 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: K 60 MET cc_start: 0.6609 (mmm) cc_final: 0.6353 (mmt) REVERT: L 4 THR cc_start: 0.8006 (p) cc_final: 0.7770 (m) outliers start: 13 outliers final: 10 residues processed: 147 average time/residue: 0.3466 time to fit residues: 73.4256 Evaluate side-chains 149 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7822 Z= 0.296 Angle : 0.552 7.059 10565 Z= 0.298 Chirality : 0.039 0.205 1251 Planarity : 0.003 0.047 1321 Dihedral : 6.778 55.304 1127 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.44 % Allowed : 15.54 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 999 helix: 1.88 (0.19), residues: 754 sheet: -0.64 (0.56), residues: 91 loop : -1.61 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.003 0.001 HIS G 82 PHE 0.016 0.002 PHE H 45 TYR 0.013 0.002 TYR G 44 ARG 0.007 0.001 ARG G 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: K 60 MET cc_start: 0.6506 (mmm) cc_final: 0.6234 (mmt) REVERT: L 4 THR cc_start: 0.8006 (p) cc_final: 0.7782 (m) REVERT: L 51 ILE cc_start: 0.7850 (mm) cc_final: 0.7591 (mt) outliers start: 11 outliers final: 11 residues processed: 141 average time/residue: 0.3309 time to fit residues: 68.1199 Evaluate side-chains 147 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain R residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105997 restraints weight = 30455.467| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.75 r_work: 0.3170 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7822 Z= 0.172 Angle : 0.490 6.044 10565 Z= 0.261 Chirality : 0.037 0.160 1251 Planarity : 0.003 0.050 1321 Dihedral : 6.399 52.964 1127 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.04 % Allowed : 15.93 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.27), residues: 999 helix: 2.17 (0.19), residues: 754 sheet: -0.64 (0.56), residues: 91 loop : -1.38 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 82 PHE 0.019 0.001 PHE K 54 TYR 0.014 0.001 TYR G 44 ARG 0.007 0.000 ARG G 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.97 seconds wall clock time: 73 minutes 0.14 seconds (4380.14 seconds total)