Starting phenix.real_space_refine on Fri Feb 16 15:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg7_11195/02_2024/6zg7_11195_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg7_11195/02_2024/6zg7_11195.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/6zg7_11195/02_2024/6zg7_11195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg7_11195/02_2024/6zg7_11195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg7_11195/02_2024/6zg7_11195_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zg7_11195/02_2024/6zg7_11195_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 41 5.16 5 C 5014 2.51 5 N 1260 2.21 5 O 1420 1.98 5 H 7852 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "G ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 224": "OE1" <-> "OE2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H ASP 69": "OD1" <-> "OD2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 118": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 1": "OD1" <-> "OD2" Residue "R PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 3": "OD1" <-> "OD2" Residue "M TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 3": "OD1" <-> "OD2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 "Q PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15587 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: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1958 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} 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: "R" 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: "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: 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: "M" 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: "N" 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: "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: 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: "O" 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 Time building chain proxies: 6.79, per 1000 atoms: 0.44 Number of scatterers: 15587 At special positions: 0 Unit cell: (70.216, 72.312, 188.64, 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 41 16.00 O 1420 8.00 N 1260 7.00 C 5014 6.00 H 7852 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: 12.20 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: 31 helices and 3 sheets defined 71.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'G' and resid 3 through 54 removed outlier: 3.821A pdb=" N ARG G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.763A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA G 50 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.533A pdb=" N LYS G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 120 removed outlier: 4.843A pdb=" N ARG G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR G 119 " --> pdb=" O ILE G 115 " (cutoff:3.500A) 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: 4.336A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (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: 4.377A 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 3 through 6 No H-bonds generated for 'chain 'I' and resid 3 through 6' Processing helix chain 'I' and resid 11 through 24 Processing helix chain 'I' and resid 28 through 35 removed outlier: 4.476A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 38 removed outlier: 3.830A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 72 removed outlier: 3.980A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 15 through 38 removed outlier: 3.720A pdb=" N GLY K 20 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 72 removed outlier: 3.758A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 14 removed outlier: 3.849A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 38 removed outlier: 3.565A pdb=" N GLY L 20 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR L 27 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG L 38 " --> pdb=" O GLY L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 72 Processing helix chain 'M' and resid 3 through 38 removed outlier: 5.446A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 72 removed outlier: 4.143A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.663A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 38 removed outlier: 3.824A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.837A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL N 67 " --> pdb=" O PHE N 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 37 removed outlier: 4.129A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 72 removed outlier: 3.653A pdb=" N GLY P 61 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 4.788A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE Q 9 " --> pdb=" O ALA Q 5 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY Q 26 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 74 removed outlier: 4.355A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 4.259A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 72 removed outlier: 3.955A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 172 through 179 removed outlier: 5.432A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 104 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 4.577A 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 22 Processing sheet with id= C, first strand: chain 'H' and resid 45 through 47 removed outlier: 6.729A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) 591 hydrogen bonds defined for protein. 1653 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: 6.08 Time building geometry restraints manager: 12.58 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: 7842 1.03 - 1.23: 30 1.23 - 1.42: 3177 1.42 - 1.61: 4581 1.61 - 1.81: 72 Bond restraints: 15702 Sorted by residual: bond pdb=" N GLN H 15 " pdb=" CA GLN H 15 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" N GLN H 15 " pdb=" H GLN H 15 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" N M3L N 43 " pdb=" CA M3L N 43 " ideal model delta sigma weight residual 1.458 1.432 0.026 1.90e-02 2.77e+03 1.83e+00 bond pdb=" N M3L Q 43 " pdb=" CA M3L Q 43 " ideal model delta sigma weight residual 1.458 1.435 0.023 1.90e-02 2.77e+03 1.47e+00 bond pdb=" N M3L R 43 " pdb=" CA M3L R 43 " ideal model delta sigma weight residual 1.458 1.435 0.023 1.90e-02 2.77e+03 1.42e+00 ... (remaining 15697 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.73: 84 105.73 - 112.79: 18602 112.79 - 119.84: 4158 119.84 - 126.90: 5477 126.90 - 133.95: 26 Bond angle restraints: 28347 Sorted by residual: angle pdb=" N M3L K 43 " pdb=" CA M3L K 43 " pdb=" C M3L K 43 " ideal model delta sigma weight residual 111.00 119.68 -8.68 2.80e+00 1.28e-01 9.61e+00 angle pdb=" N VAL K 18 " pdb=" CA VAL K 18 " pdb=" C VAL K 18 " ideal model delta sigma weight residual 113.07 108.91 4.16 1.37e+00 5.33e-01 9.23e+00 angle pdb=" N GLN K 44 " pdb=" CA GLN K 44 " pdb=" C GLN K 44 " ideal model delta sigma weight residual 111.00 103.60 7.40 2.80e+00 1.28e-01 6.98e+00 angle pdb=" N VAL L 16 " pdb=" CA VAL L 16 " pdb=" C VAL L 16 " ideal model delta sigma weight residual 112.98 109.82 3.16 1.25e+00 6.40e-01 6.39e+00 angle pdb=" C SER M 57 " pdb=" N GLU M 58 " pdb=" CA GLU M 58 " ideal model delta sigma weight residual 121.18 116.50 4.68 1.98e+00 2.55e-01 5.58e+00 ... (remaining 28342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6502 17.97 - 35.94: 566 35.94 - 53.91: 202 53.91 - 71.87: 69 71.87 - 89.84: 13 Dihedral angle restraints: 7352 sinusoidal: 3910 harmonic: 3442 Sorted by residual: dihedral pdb=" CA MET O 60 " pdb=" C MET O 60 " pdb=" N GLY O 61 " pdb=" CA GLY O 61 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP R 3 " pdb=" C ASP R 3 " pdb=" N THR R 4 " pdb=" CA THR R 4 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA M3L K 43 " pdb=" C M3L K 43 " pdb=" N GLN K 44 " pdb=" CA GLN K 44 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 7349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 712 0.029 - 0.057: 360 0.057 - 0.086: 124 0.086 - 0.115: 38 0.115 - 0.143: 21 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA PRO Q 40 " pdb=" N PRO Q 40 " pdb=" C PRO Q 40 " pdb=" CB PRO Q 40 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-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 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA M3L K 43 " pdb=" N M3L K 43 " pdb=" C M3L K 43 " pdb=" CB M3L K 43 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1252 not shown) Planarity restraints: 2336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 44 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLN K 44 " 0.062 2.00e-02 2.50e+03 pdb=" O GLN K 44 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN K 45 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 20 " -0.014 2.00e-02 2.50e+03 1.05e-02 3.31e+00 pdb=" CG PHE H 20 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 20 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE H 20 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 20 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE H 20 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 20 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE H 20 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE H 20 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE H 20 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE H 20 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE H 20 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 47 " -0.014 2.00e-02 2.50e+03 7.82e-03 1.83e+00 pdb=" CG PHE N 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE N 47 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE N 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE N 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE N 47 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE N 47 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE N 47 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE N 47 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE N 47 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE N 47 " 0.000 2.00e-02 2.50e+03 ... (remaining 2333 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 977 2.19 - 2.79: 32660 2.79 - 3.40: 45426 3.40 - 4.00: 58076 4.00 - 4.60: 92213 Nonbonded interactions: 229352 Sorted by model distance: nonbonded pdb=" OD1 ASN H 85 " pdb="HE22 GLN H 91 " model vdw 1.591 1.850 nonbonded pdb=" O ASP Q 1 " pdb=" HG1 THR Q 4 " model vdw 1.624 1.850 nonbonded pdb=" O PRO G 136 " pdb=" HZ3 LYS G 218 " model vdw 1.649 1.850 nonbonded pdb=" O HIS G 66 " pdb=" HH TYR G 153 " model vdw 1.673 1.850 nonbonded pdb=" OD2 ASP H 37 " pdb=" HG SER Q 41 " model vdw 1.675 1.850 ... (remaining 229347 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 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: 5.710 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: 0.240 Extract box with map and model: 26.300 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 51.370 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.045 7850 Z= 0.390 Angle : 0.661 8.681 10600 Z= 0.364 Chirality : 0.040 0.143 1255 Planarity : 0.003 0.036 1324 Dihedral : 14.313 89.843 2727 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.05 (0.27), residues: 1002 helix: 0.71 (0.19), residues: 762 sheet: -2.35 (0.56), residues: 84 loop : -1.90 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.005 0.001 HIS H 51 PHE 0.031 0.002 PHE H 20 TYR 0.014 0.002 TYR G 193 ARG 0.005 0.001 ARG H 128 *********************** 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 147 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: G 232 MET cc_start: 0.8474 (mmm) cc_final: 0.8258 (mmt) REVERT: H 136 GLU cc_start: 0.7734 (tt0) cc_final: 0.7532 (tt0) REVERT: I 14 TYR cc_start: 0.8997 (t80) cc_final: 0.8755 (t80) REVERT: I 29 GLU cc_start: 0.7588 (pp20) cc_final: 0.7321 (pp20) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.3254 time to fit residues: 71.6091 Evaluate side-chains 124 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7850 Z= 0.297 Angle : 0.549 5.065 10600 Z= 0.306 Chirality : 0.037 0.142 1255 Planarity : 0.004 0.052 1324 Dihedral : 6.054 58.165 1130 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.56 % Allowed : 7.27 % Favored : 91.17 % 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: 0.23 (0.27), residues: 1002 helix: 0.92 (0.19), residues: 746 sheet: -2.27 (0.56), residues: 83 loop : -1.62 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.004 0.001 HIS H 51 PHE 0.020 0.001 PHE H 20 TYR 0.013 0.001 TYR I 11 ARG 0.002 0.000 ARG P 38 *********************** 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 141 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.223 Fit side-chains REVERT: G 232 MET cc_start: 0.8497 (mmm) cc_final: 0.8278 (mmt) REVERT: H 136 GLU cc_start: 0.7745 (tt0) cc_final: 0.7525 (tt0) REVERT: I 14 TYR cc_start: 0.8968 (t80) cc_final: 0.8670 (t80) outliers start: 12 outliers final: 11 residues processed: 137 average time/residue: 0.3031 time to fit residues: 63.2221 Evaluate side-chains 137 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7850 Z= 0.244 Angle : 0.509 4.606 10600 Z= 0.280 Chirality : 0.036 0.143 1255 Planarity : 0.004 0.043 1324 Dihedral : 5.843 58.995 1130 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.08 % Allowed : 10.00 % Favored : 87.92 % 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: 0.50 (0.27), residues: 1002 helix: 1.10 (0.19), residues: 745 sheet: -2.30 (0.54), residues: 86 loop : -1.35 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 PHE 0.016 0.001 PHE H 20 TYR 0.012 0.001 TYR I 11 ARG 0.003 0.000 ARG L 38 *********************** 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 141 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.097 Fit side-chains REVERT: G 232 MET cc_start: 0.8531 (mmm) cc_final: 0.8277 (mmt) outliers start: 16 outliers final: 16 residues processed: 134 average time/residue: 0.3027 time to fit residues: 61.4078 Evaluate side-chains 136 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7850 Z= 0.219 Angle : 0.490 4.913 10600 Z= 0.268 Chirality : 0.036 0.143 1255 Planarity : 0.004 0.041 1324 Dihedral : 5.635 59.492 1130 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.21 % Allowed : 11.04 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1002 helix: 1.31 (0.19), residues: 745 sheet: -2.42 (0.52), residues: 93 loop : -1.10 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 PHE 0.016 0.001 PHE H 20 TYR 0.012 0.001 TYR I 11 ARG 0.002 0.000 ARG L 38 *********************** 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 152 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.170 Fit side-chains REVERT: G 232 MET cc_start: 0.8552 (mmm) cc_final: 0.8291 (mmt) outliers start: 17 outliers final: 15 residues processed: 143 average time/residue: 0.3377 time to fit residues: 74.2024 Evaluate side-chains 140 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7850 Z= 0.335 Angle : 0.546 5.246 10600 Z= 0.300 Chirality : 0.037 0.139 1255 Planarity : 0.004 0.048 1324 Dihedral : 5.845 58.849 1130 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.60 % Allowed : 13.38 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 1002 helix: 1.09 (0.19), residues: 745 sheet: -2.34 (0.54), residues: 85 loop : -1.31 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 PHE 0.022 0.002 PHE H 20 TYR 0.013 0.002 TYR G 193 ARG 0.002 0.000 ARG P 38 *********************** 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 151 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.318 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 143 average time/residue: 0.3062 time to fit residues: 66.5040 Evaluate side-chains 145 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7850 Z= 0.253 Angle : 0.508 5.759 10600 Z= 0.278 Chirality : 0.036 0.144 1255 Planarity : 0.004 0.040 1324 Dihedral : 5.735 59.429 1130 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.73 % Allowed : 14.68 % Favored : 82.60 % 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: 0.74 (0.27), residues: 1002 helix: 1.26 (0.19), residues: 745 sheet: -2.28 (0.53), residues: 87 loop : -1.13 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 PHE 0.018 0.001 PHE H 20 TYR 0.012 0.001 TYR I 11 ARG 0.003 0.000 ARG L 38 *********************** 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 153 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.350 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 21 residues processed: 144 average time/residue: 0.3024 time to fit residues: 66.2146 Evaluate side-chains 146 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.0770 chunk 60 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 234 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7850 Z= 0.154 Angle : 0.457 5.584 10600 Z= 0.248 Chirality : 0.035 0.147 1255 Planarity : 0.003 0.030 1324 Dihedral : 5.286 58.825 1130 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.95 % Allowed : 15.84 % Favored : 82.21 % 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: 1.34 (0.28), residues: 1002 helix: 1.64 (0.20), residues: 750 sheet: -2.28 (0.53), residues: 91 loop : -0.51 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.001 0.000 HIS H 66 PHE 0.011 0.001 PHE Q 54 TYR 0.009 0.001 TYR G 31 ARG 0.002 0.000 ARG L 38 *********************** 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 145 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.228 Fit side-chains REVERT: L 39 ASN cc_start: 0.8702 (t0) cc_final: 0.8444 (t0) outliers start: 15 outliers final: 12 residues processed: 135 average time/residue: 0.3010 time to fit residues: 62.1000 Evaluate side-chains 137 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 234 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7850 Z= 0.271 Angle : 0.508 5.073 10600 Z= 0.277 Chirality : 0.036 0.139 1255 Planarity : 0.004 0.041 1324 Dihedral : 5.485 57.194 1130 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.21 % Allowed : 15.97 % Favored : 81.82 % 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: 1.15 (0.28), residues: 1002 helix: 1.51 (0.20), residues: 745 sheet: -2.17 (0.54), residues: 87 loop : -0.71 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 PHE 0.018 0.001 PHE H 20 TYR 0.012 0.001 TYR I 11 ARG 0.003 0.000 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.226 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 16 residues processed: 135 average time/residue: 0.3097 time to fit residues: 63.4409 Evaluate side-chains 141 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 234 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7850 Z= 0.265 Angle : 0.510 7.078 10600 Z= 0.277 Chirality : 0.036 0.140 1255 Planarity : 0.004 0.036 1324 Dihedral : 5.530 56.666 1130 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.95 % Allowed : 16.62 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 1002 helix: 1.45 (0.20), residues: 745 sheet: -2.19 (0.54), residues: 87 loop : -0.72 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 PHE 0.018 0.001 PHE H 20 TYR 0.012 0.001 TYR I 11 ARG 0.002 0.000 ARG L 38 *********************** 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 143 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.309 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 134 average time/residue: 0.3239 time to fit residues: 65.9802 Evaluate side-chains 141 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 234 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7850 Z= 0.281 Angle : 0.519 5.022 10600 Z= 0.282 Chirality : 0.037 0.163 1255 Planarity : 0.004 0.036 1324 Dihedral : 5.580 55.871 1130 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.34 % Allowed : 16.23 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.28), residues: 1002 helix: 1.42 (0.20), residues: 745 sheet: -2.24 (0.54), residues: 87 loop : -0.73 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.004 0.001 HIS H 51 PHE 0.018 0.001 PHE H 20 TYR 0.012 0.001 TYR I 11 ARG 0.002 0.000 ARG L 38 ********************** 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 144 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.180 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 17 residues processed: 135 average time/residue: 0.3025 time to fit residues: 61.6195 Evaluate side-chains 143 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 58 GLU 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: 1.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 234 ASN ** H 32 ASN ** 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 = 0.3540 r_free = 0.3540 target = 0.125206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102228 restraints weight = 31103.799| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.71 r_work: 0.3102 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7850 Z= 0.295 Angle : 0.529 5.007 10600 Z= 0.288 Chirality : 0.037 0.162 1255 Planarity : 0.004 0.035 1324 Dihedral : 5.607 54.655 1130 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.47 % Allowed : 16.23 % Favored : 81.30 % 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: 0.91 (0.27), residues: 1002 helix: 1.34 (0.19), residues: 746 sheet: -2.26 (0.53), residues: 87 loop : -0.83 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 4 HIS 0.004 0.001 HIS H 51 PHE 0.019 0.001 PHE H 20 TYR 0.012 0.002 TYR G 193 ARG 0.002 0.000 ARG L 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.04 seconds wall clock time: 71 minutes 42.28 seconds (4302.28 seconds total)