Starting phenix.real_space_refine (version: dev) on Tue Apr 5 05:03:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/04_2022/6n1h_8902.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/04_2022/6n1h_8902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/04_2022/6n1h_8902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/04_2022/6n1h_8902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/04_2022/6n1h_8902.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/04_2022/6n1h_8902.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 119": "NH1" <-> "NH2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "E ARG 119": "NH1" <-> "NH2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 194": "NH1" <-> "NH2" Residue "G ARG 119": "NH1" <-> "NH2" Residue "G TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 194": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 194": "NH1" <-> "NH2" Residue "I ARG 119": "NH1" <-> "NH2" Residue "I TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 194": "NH1" <-> "NH2" Residue "J ARG 119": "NH1" <-> "NH2" Residue "J TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 194": "NH1" <-> "NH2" Residue "K ARG 119": "NH1" <-> "NH2" Residue "K TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 194": "NH1" <-> "NH2" Residue "L ARG 119": "NH1" <-> "NH2" Residue "L TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 194": "NH1" <-> "NH2" Residue "M ARG 119": "NH1" <-> "NH2" Residue "M TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 194": "NH1" <-> "NH2" Residue "N ARG 119": "NH1" <-> "NH2" Residue "N TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "O ARG 119": "NH1" <-> "NH2" Residue "O TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 194": "NH1" <-> "NH2" Residue "P ARG 119": "NH1" <-> "NH2" Residue "P TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 194": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10991 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 686 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 687 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.60, per 1000 atoms: 0.60 Number of scatterers: 10991 At special positions: 0 Unit cell: (92.4, 91.08, 113.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 2000 8.00 N 1919 7.00 C 7040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2622 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 0 sheets defined 88.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.032A pdb=" N ASP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.733A pdb=" N MET A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.678A pdb=" N ASP A 175 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 149 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 150 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP B 175 " --> pdb=" O TRP B 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 194 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.891A pdb=" N ASP C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 150 removed outlier: 3.540A pdb=" N ALA C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 149 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.733A pdb=" N MET C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP C 175 " --> pdb=" O TRP C 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.540A pdb=" N ALA D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 150 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET D 159 " --> pdb=" O ASN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP D 175 " --> pdb=" O TRP D 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG E 150 " --> pdb=" O TYR E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP E 175 " --> pdb=" O TRP E 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 149 " --> pdb=" O GLN F 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG F 150 " --> pdb=" O TYR F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 163 removed outlier: 3.733A pdb=" N MET F 159 " --> pdb=" O ASN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP F 175 " --> pdb=" O TRP F 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 137 removed outlier: 3.891A pdb=" N ASP G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA G 148 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL G 149 " --> pdb=" O GLN G 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 150 " --> pdb=" O TYR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 163 removed outlier: 3.733A pdb=" N MET G 159 " --> pdb=" O ASN G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 169 Processing helix chain 'G' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP G 175 " --> pdb=" O TRP G 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU G 176 " --> pdb=" O THR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 194 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 137 removed outlier: 3.891A pdb=" N ASP H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA H 148 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL H 149 " --> pdb=" O GLN H 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG H 150 " --> pdb=" O TYR H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET H 159 " --> pdb=" O ASN H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP H 175 " --> pdb=" O TRP H 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU H 176 " --> pdb=" O THR H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 194 Processing helix chain 'I' and resid 113 through 118 Processing helix chain 'I' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP I 134 " --> pdb=" O GLU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL I 149 " --> pdb=" O GLN I 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG I 150 " --> pdb=" O TYR I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET I 159 " --> pdb=" O ASN I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 169 Processing helix chain 'I' and resid 170 through 185 removed outlier: 3.678A pdb=" N ASP I 175 " --> pdb=" O TRP I 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU I 176 " --> pdb=" O THR I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 194 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA J 124 " --> pdb=" O ALA J 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL J 126 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 137 removed outlier: 3.891A pdb=" N ASP J 134 " --> pdb=" O GLU J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 150 removed outlier: 3.542A pdb=" N ALA J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL J 149 " --> pdb=" O GLN J 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG J 150 " --> pdb=" O TYR J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET J 159 " --> pdb=" O ASN J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP J 175 " --> pdb=" O TRP J 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU J 176 " --> pdb=" O THR J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 194 Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA K 124 " --> pdb=" O ALA K 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP K 134 " --> pdb=" O GLU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA K 148 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL K 149 " --> pdb=" O GLN K 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG K 150 " --> pdb=" O TYR K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET K 159 " --> pdb=" O ASN K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP K 175 " --> pdb=" O TRP K 171 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU K 176 " --> pdb=" O THR K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 194 Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'L' and resid 118 through 126 removed outlier: 3.582A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL L 126 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 removed outlier: 3.891A pdb=" N ASP L 134 " --> pdb=" O GLU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL L 149 " --> pdb=" O GLN L 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG L 150 " --> pdb=" O TYR L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET L 159 " --> pdb=" O ASN L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 170 through 185 removed outlier: 3.678A pdb=" N ASP L 175 " --> pdb=" O TRP L 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU L 176 " --> pdb=" O THR L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 194 Processing helix chain 'M' and resid 113 through 118 Processing helix chain 'M' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL M 126 " --> pdb=" O LEU M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP M 134 " --> pdb=" O GLU M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL M 149 " --> pdb=" O GLN M 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG M 150 " --> pdb=" O TYR M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 3.732A pdb=" N MET M 159 " --> pdb=" O ASN M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 170 through 185 removed outlier: 3.680A pdb=" N ASP M 175 " --> pdb=" O TRP M 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU M 176 " --> pdb=" O THR M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 194 Processing helix chain 'N' and resid 113 through 118 Processing helix chain 'N' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA N 124 " --> pdb=" O ALA N 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP N 134 " --> pdb=" O GLU N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA N 148 " --> pdb=" O GLU N 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL N 149 " --> pdb=" O GLN N 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG N 150 " --> pdb=" O TYR N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 163 removed outlier: 3.733A pdb=" N MET N 159 " --> pdb=" O ASN N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP N 175 " --> pdb=" O TRP N 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 194 Processing helix chain 'O' and resid 113 through 118 Processing helix chain 'O' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA O 124 " --> pdb=" O ALA O 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 137 removed outlier: 3.892A pdb=" N ASP O 134 " --> pdb=" O GLU O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 150 removed outlier: 3.541A pdb=" N ALA O 148 " --> pdb=" O GLU O 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL O 149 " --> pdb=" O GLN O 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG O 150 " --> pdb=" O TYR O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 163 removed outlier: 3.733A pdb=" N MET O 159 " --> pdb=" O ASN O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 170 through 185 removed outlier: 3.679A pdb=" N ASP O 175 " --> pdb=" O TRP O 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU O 176 " --> pdb=" O THR O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 194 Processing helix chain 'P' and resid 113 through 118 Processing helix chain 'P' and resid 118 through 126 removed outlier: 3.583A pdb=" N ALA P 124 " --> pdb=" O ALA P 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL P 126 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 137 removed outlier: 3.891A pdb=" N ASP P 134 " --> pdb=" O GLU P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 150 removed outlier: 3.542A pdb=" N ALA P 148 " --> pdb=" O GLU P 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL P 149 " --> pdb=" O GLN P 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG P 150 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 154 through 163 removed outlier: 3.733A pdb=" N MET P 159 " --> pdb=" O ASN P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 170 through 185 removed outlier: 3.678A pdb=" N ASP P 175 " --> pdb=" O TRP P 171 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU P 176 " --> pdb=" O THR P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 194 528 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3417 1.34 - 1.45: 1661 1.45 - 1.57: 6121 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 11247 Sorted by residual: bond pdb=" C THR E 166 " pdb=" N PRO E 167 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.67e+00 bond pdb=" C THR I 166 " pdb=" N PRO I 167 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.65e+00 bond pdb=" C THR K 166 " pdb=" N PRO K 167 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.61e+00 bond pdb=" C THR P 166 " pdb=" N PRO P 167 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.19e-02 7.06e+03 2.50e+00 bond pdb=" C THR G 166 " pdb=" N PRO G 167 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.19e-02 7.06e+03 2.50e+00 ... (remaining 11242 not shown) Histogram of bond angle deviations from ideal: 101.18 - 107.74: 475 107.74 - 114.29: 6146 114.29 - 120.85: 5344 120.85 - 127.40: 3119 127.40 - 133.96: 178 Bond angle restraints: 15262 Sorted by residual: angle pdb=" C THR A 154 " pdb=" N ASN A 155 " pdb=" CA ASN A 155 " ideal model delta sigma weight residual 120.06 126.50 -6.44 1.19e+00 7.06e-01 2.93e+01 angle pdb=" C THR H 154 " pdb=" N ASN H 155 " pdb=" CA ASN H 155 " ideal model delta sigma weight residual 120.06 126.50 -6.44 1.19e+00 7.06e-01 2.93e+01 angle pdb=" C THR N 154 " pdb=" N ASN N 155 " pdb=" CA ASN N 155 " ideal model delta sigma weight residual 120.06 126.49 -6.43 1.19e+00 7.06e-01 2.92e+01 angle pdb=" C THR I 154 " pdb=" N ASN I 155 " pdb=" CA ASN I 155 " ideal model delta sigma weight residual 120.06 126.48 -6.42 1.19e+00 7.06e-01 2.91e+01 angle pdb=" C THR L 154 " pdb=" N ASN L 155 " pdb=" CA ASN L 155 " ideal model delta sigma weight residual 120.06 126.48 -6.42 1.19e+00 7.06e-01 2.91e+01 ... (remaining 15257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 6319 14.34 - 28.68: 239 28.68 - 43.02: 143 43.02 - 57.35: 32 57.35 - 71.69: 32 Dihedral angle restraints: 6765 sinusoidal: 2783 harmonic: 3982 Sorted by residual: dihedral pdb=" CA GLU C 152 " pdb=" C GLU C 152 " pdb=" N PRO C 153 " pdb=" CA PRO C 153 " ideal model delta harmonic sigma weight residual -180.00 -157.14 -22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLU L 152 " pdb=" C GLU L 152 " pdb=" N PRO L 153 " pdb=" CA PRO L 153 " ideal model delta harmonic sigma weight residual -180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLU J 152 " pdb=" C GLU J 152 " pdb=" N PRO J 153 " pdb=" CA PRO J 153 " ideal model delta harmonic sigma weight residual 180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 6762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1326 0.054 - 0.108: 230 0.108 - 0.163: 91 0.163 - 0.217: 16 0.217 - 0.271: 16 Chirality restraints: 1679 Sorted by residual: chirality pdb=" CG LEU J 112 " pdb=" CB LEU J 112 " pdb=" CD1 LEU J 112 " pdb=" CD2 LEU J 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CG LEU C 112 " pdb=" CB LEU C 112 " pdb=" CD1 LEU C 112 " pdb=" CD2 LEU C 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU F 112 " pdb=" CB LEU F 112 " pdb=" CD1 LEU F 112 " pdb=" CD2 LEU F 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1676 not shown) Planarity restraints: 1936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR O 166 " 0.042 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO O 167 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO O 167 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO O 167 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 166 " 0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO E 167 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 167 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 167 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 166 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO G 167 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 167 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 167 " -0.035 5.00e-02 4.00e+02 ... (remaining 1933 not shown) Histogram of nonbonded interaction distances: 0.66 - 1.51: 6 1.51 - 2.35: 74 2.35 - 3.20: 9700 3.20 - 4.05: 28380 4.05 - 4.90: 53795 Warning: very small nonbonded interaction distances. Nonbonded interactions: 91955 Sorted by model distance: nonbonded pdb=" OD2 ASP B 134 " pdb=" NH1 ARG E 160 " model vdw 0.657 2.520 nonbonded pdb=" CG ASP B 134 " pdb=" NH1 ARG E 160 " model vdw 1.100 3.350 nonbonded pdb=" OD2 ASP B 134 " pdb=" CZ ARG E 160 " model vdw 1.135 3.270 nonbonded pdb=" CG2 THR B 154 " pdb=" CA ALA C 148 " model vdw 1.186 3.890 nonbonded pdb=" OD2 ASP K 134 " pdb=" NH1 ARG N 160 " model vdw 1.206 2.520 ... (remaining 91950 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 'A' selection = (chain 'B' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'C' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'D' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'E' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'F' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'G' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'H' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'I' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'J' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'K' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'L' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'M' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'N' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'O' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) selection = (chain 'P' and ((resid 112 and (name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or resid 113 through 194)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 7040 2.51 5 N 1919 2.21 5 O 2000 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.570 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 31.750 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4585 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 0.055 11247 Z= 0.385 Angle : 1.129 10.738 15262 Z= 0.652 Chirality : 0.058 0.271 1679 Planarity : 0.008 0.062 1936 Dihedral : 12.227 71.692 4143 Min Nonbonded Distance : 0.657 Molprobity Statistics. All-atom Clashscore : 31.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.22 (0.10), residues: 1296 helix: -4.65 (0.05), residues: 976 sheet: None (None), residues: 0 loop : -4.20 (0.22), residues: 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 219 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 37 residues processed: 264 average time/residue: 0.2320 time to fit residues: 86.4520 Evaluate side-chains 180 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 37 average time/residue: 0.0955 time to fit residues: 8.5774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 147 GLN E 118 HIS ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN H 118 HIS I 113 HIS J 118 HIS J 128 ASN J 185 GLN K 118 HIS L 145 GLN M 118 HIS N 128 ASN N 185 GLN O 117 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 11247 Z= 0.242 Angle : 0.737 9.508 15262 Z= 0.383 Chirality : 0.043 0.181 1679 Planarity : 0.009 0.096 1936 Dihedral : 5.887 24.766 1456 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.79 % Favored : 93.13 % Rotamer Outliers : 4.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.18), residues: 1296 helix: -2.49 (0.12), residues: 993 sheet: None (None), residues: 0 loop : -2.94 (0.29), residues: 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 38 residues processed: 270 average time/residue: 0.2228 time to fit residues: 85.2677 Evaluate side-chains 214 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 38 average time/residue: 0.0947 time to fit residues: 8.6083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 170 ASN D 185 GLN E 113 HIS F 128 ASN ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN G 128 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN L 155 ASN M 185 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.8992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.125 11247 Z= 0.275 Angle : 0.770 15.789 15262 Z= 0.394 Chirality : 0.043 0.161 1679 Planarity : 0.008 0.103 1936 Dihedral : 5.225 23.683 1456 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 5.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.21), residues: 1296 helix: -1.12 (0.16), residues: 918 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 267 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 42 residues processed: 316 average time/residue: 0.2319 time to fit residues: 102.7921 Evaluate side-chains 247 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 32 residues processed: 42 average time/residue: 0.0979 time to fit residues: 9.4974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.0030 chunk 33 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN G 128 ASN H 145 GLN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 1.0153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 11247 Z= 0.171 Angle : 0.639 12.652 15262 Z= 0.322 Chirality : 0.040 0.161 1679 Planarity : 0.007 0.098 1936 Dihedral : 4.828 22.395 1456 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 3.89 % 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 (0.23), residues: 1296 helix: -0.02 (0.17), residues: 919 sheet: None (None), residues: 0 loop : -1.50 (0.29), residues: 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 1.396 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 46 outliers final: 36 residues processed: 284 average time/residue: 0.2295 time to fit residues: 92.0832 Evaluate side-chains 255 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 36 average time/residue: 0.0975 time to fit residues: 8.6952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN F 128 ASN G 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 1.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 11247 Z= 0.190 Angle : 0.605 9.441 15262 Z= 0.307 Chirality : 0.040 0.141 1679 Planarity : 0.006 0.102 1936 Dihedral : 4.641 23.510 1456 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 3.63 % 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: -0.01 (0.23), residues: 1296 helix: 0.59 (0.18), residues: 921 sheet: None (None), residues: 0 loop : -1.38 (0.30), residues: 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 249 time to evaluate : 1.442 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 36 residues processed: 275 average time/residue: 0.2459 time to fit residues: 93.4411 Evaluate side-chains 259 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 36 average time/residue: 0.1007 time to fit residues: 8.6900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 0.0020 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 185 GLN C 147 GLN F 128 ASN H 145 GLN N 128 ASN O 117 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 1.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 11247 Z= 0.208 Angle : 0.621 11.482 15262 Z= 0.317 Chirality : 0.040 0.155 1679 Planarity : 0.006 0.099 1936 Dihedral : 4.721 24.062 1456 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1296 helix: 0.97 (0.18), residues: 877 sheet: None (None), residues: 0 loop : -1.18 (0.29), residues: 419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 263 time to evaluate : 1.507 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 45 outliers final: 38 residues processed: 291 average time/residue: 0.2405 time to fit residues: 96.4437 Evaluate side-chains 268 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 230 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 38 average time/residue: 0.0948 time to fit residues: 8.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 123 optimal weight: 0.0670 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 HIS C 147 GLN F 128 ASN G 117 GLN H 113 HIS K 128 ASN N 128 ASN O 117 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 1.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 11247 Z= 0.205 Angle : 0.618 12.535 15262 Z= 0.316 Chirality : 0.040 0.143 1679 Planarity : 0.006 0.104 1936 Dihedral : 4.599 25.658 1456 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 3.38 % 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: 0.79 (0.24), residues: 1296 helix: 1.29 (0.18), residues: 877 sheet: None (None), residues: 0 loop : -1.09 (0.29), residues: 419 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 242 time to evaluate : 1.358 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 40 outliers final: 35 residues processed: 269 average time/residue: 0.2289 time to fit residues: 86.7954 Evaluate side-chains 259 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 35 average time/residue: 0.0943 time to fit residues: 8.1271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.0270 chunk 96 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN H 113 HIS H 145 GLN O 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 1.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.183 11247 Z= 0.230 Angle : 0.625 14.843 15262 Z= 0.328 Chirality : 0.039 0.135 1679 Planarity : 0.006 0.114 1936 Dihedral : 4.494 23.317 1456 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer Outliers : 3.13 % 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: 0.99 (0.24), residues: 1296 helix: 1.47 (0.18), residues: 877 sheet: None (None), residues: 0 loop : -1.06 (0.30), residues: 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 1.471 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 37 outliers final: 36 residues processed: 252 average time/residue: 0.2377 time to fit residues: 84.1307 Evaluate side-chains 252 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 36 average time/residue: 0.0972 time to fit residues: 8.5496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.5980 chunk 107 optimal weight: 0.0980 chunk 114 optimal weight: 0.1980 chunk 69 optimal weight: 0.0040 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 185 GLN G 117 GLN H 113 HIS N 128 ASN O 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 1.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.129 11247 Z= 0.181 Angle : 0.594 14.544 15262 Z= 0.304 Chirality : 0.039 0.125 1679 Planarity : 0.006 0.113 1936 Dihedral : 4.369 23.599 1456 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1296 helix: 1.65 (0.19), residues: 876 sheet: None (None), residues: 0 loop : -0.96 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 1.388 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 36 outliers final: 34 residues processed: 253 average time/residue: 0.2309 time to fit residues: 82.8178 Evaluate side-chains 249 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 34 average time/residue: 0.1059 time to fit residues: 8.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 127 optimal weight: 0.0570 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 108 optimal weight: 0.0870 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN H 113 HIS O 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 1.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.147 11247 Z= 0.186 Angle : 0.606 14.356 15262 Z= 0.306 Chirality : 0.040 0.182 1679 Planarity : 0.006 0.121 1936 Dihedral : 4.398 21.709 1456 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1296 helix: 1.70 (0.19), residues: 877 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 1.379 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 33 outliers final: 32 residues processed: 242 average time/residue: 0.2486 time to fit residues: 84.9784 Evaluate side-chains 243 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 32 average time/residue: 0.1011 time to fit residues: 8.0912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 104 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN P 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.138622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.126309 restraints weight = 13874.865| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.19 r_work: 0.3304 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 1.12 restraints_weight: 0.2500 r_work: 0.3277 rms_B_bonded: 1.31 restraints_weight: 0.1250 r_work: 0.3259 rms_B_bonded: 1.58 restraints_weight: 0.0625 r_work: 0.3237 rms_B_bonded: 1.97 restraints_weight: 0.0312 r_work: 0.3209 rms_B_bonded: 2.48 restraints_weight: 0.0156 r_work: 0.3173 rms_B_bonded: 3.17 restraints_weight: 0.0078 r_work: 0.3128 rms_B_bonded: 4.10 restraints_weight: 0.0039 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 1.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 11247 Z= 0.183 Angle : 0.594 13.642 15262 Z= 0.297 Chirality : 0.040 0.180 1679 Planarity : 0.006 0.103 1936 Dihedral : 4.443 23.549 1456 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 2.87 % 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: 1.25 (0.24), residues: 1296 helix: 1.59 (0.18), residues: 921 sheet: None (None), residues: 0 loop : -1.07 (0.31), residues: 375 =============================================================================== Job complete usr+sys time: 2407.62 seconds wall clock time: 44 minutes 31.22 seconds (2671.22 seconds total)