Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 04:15:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/08_2023/6n1h_8902.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/08_2023/6n1h_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_8902/08_2023/6n1h_8902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/08_2023/6n1h_8902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/08_2023/6n1h_8902.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/08_2023/6n1h_8902.pdb" } resolution = 3.17 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 ------------------------------------------------------------------------------- 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 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. 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-1.21rc1-5044/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: 6.04, per 1000 atoms: 0.55 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: 4.38 Conformation dependent library (CDL) restraints added in 1.5 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: 1.17 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: 2.96 Time building geometry restraints manager: 4.73 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 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: 3.150 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: 0.000 Extract box with map and model: 2.000 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 31.390 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4458 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 : 32.07 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 : 1.277 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: 0.2318 time to fit residues: 86.2792 Evaluate side-chains 187 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 37 average time/residue: 0.0946 time to fit residues: 8.5259 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 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: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS 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 N 128 ASN N 185 GLN O 117 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 11247 Z= 0.252 Angle : 0.717 9.479 15262 Z= 0.366 Chirality : 0.044 0.197 1679 Planarity : 0.007 0.053 1936 Dihedral : 5.914 24.980 1456 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 4.14 % 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: -4.25 (0.17), residues: 1296 helix: -2.55 (0.12), residues: 996 sheet: None (None), residues: 0 loop : -2.96 (0.29), residues: 300 *********************** 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 283 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 39 residues processed: 270 average time/residue: 0.2247 time to fit residues: 85.5291 Evaluate side-chains 218 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 39 average time/residue: 0.0914 time to fit residues: 8.4407 ------------------------------------------------------------------------------- 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: 6.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** C 185 GLN D 128 ASN D 170 ASN D 185 GLN E 113 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 185 GLN O 128 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11247 Z= 0.202 Angle : 0.648 10.135 15262 Z= 0.329 Chirality : 0.042 0.260 1679 Planarity : 0.005 0.043 1936 Dihedral : 5.005 22.142 1456 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 4.90 % 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: -1.78 (0.21), residues: 1296 helix: -0.93 (0.16), residues: 918 sheet: None (None), residues: 0 loop : -1.42 (0.29), 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 305 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 247 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 40 residues processed: 292 average time/residue: 0.2407 time to fit residues: 98.7980 Evaluate side-chains 241 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 40 average time/residue: 0.1014 time to fit residues: 9.4714 ------------------------------------------------------------------------------- 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: 2.9990 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 61 optimal weight: 0.0670 chunk 110 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 147 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN G 185 GLN H 145 GLN I 128 ASN I 185 GLN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 ASN ** L 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.9952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 11247 Z= 0.172 Angle : 0.600 11.788 15262 Z= 0.298 Chirality : 0.041 0.182 1679 Planarity : 0.004 0.039 1936 Dihedral : 4.795 22.736 1456 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 4.31 % 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: -0.58 (0.23), residues: 1296 helix: 0.04 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 378 *********************** 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 334 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 283 time to evaluate : 1.233 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 39 residues processed: 314 average time/residue: 0.2392 time to fit residues: 104.5392 Evaluate side-chains 269 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 39 average time/residue: 0.0953 time to fit residues: 8.7682 ------------------------------------------------------------------------------- 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: 0.9990 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 113 HIS B 185 GLN D 147 GLN D 185 GLN E 118 HIS ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN M 128 ASN N 128 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 1.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11247 Z= 0.230 Angle : 0.679 10.130 15262 Z= 0.335 Chirality : 0.043 0.165 1679 Planarity : 0.005 0.040 1936 Dihedral : 4.965 24.795 1456 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -0.19 (0.23), residues: 1296 helix: 0.56 (0.17), residues: 891 sheet: None (None), residues: 0 loop : -1.57 (0.27), residues: 405 *********************** 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 321 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 273 time to evaluate : 1.404 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 48 outliers final: 35 residues processed: 307 average time/residue: 0.2687 time to fit residues: 111.5756 Evaluate side-chains 269 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 234 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 35 average time/residue: 0.0937 time to fit residues: 8.0721 ------------------------------------------------------------------------------- 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: 0.9980 chunk 111 optimal weight: 0.0770 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 128 ASN G 117 GLN H 145 GLN M 118 HIS N 118 HIS N 128 ASN O 117 GLN P 113 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 1.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11247 Z= 0.164 Angle : 0.577 9.357 15262 Z= 0.288 Chirality : 0.040 0.155 1679 Planarity : 0.004 0.039 1936 Dihedral : 4.661 22.689 1456 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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: 0.00 (0.23), residues: 1296 helix: 0.63 (0.17), residues: 966 sheet: None (None), residues: 0 loop : -1.71 (0.30), residues: 330 *********************** 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 290 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 247 time to evaluate : 1.403 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 43 outliers final: 41 residues processed: 276 average time/residue: 0.2492 time to fit residues: 95.2814 Evaluate side-chains 271 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 230 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 32 residues processed: 41 average time/residue: 0.0973 time to fit residues: 9.2701 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** F 128 ASN ** F 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 GLN ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN O 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 1.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11247 Z= 0.203 Angle : 0.606 9.484 15262 Z= 0.302 Chirality : 0.041 0.162 1679 Planarity : 0.004 0.038 1936 Dihedral : 4.771 24.838 1456 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 3.72 % 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: 0.14 (0.24), residues: 1296 helix: 0.77 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 256 *********************** 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 301 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 257 time to evaluate : 1.347 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 44 outliers final: 39 residues processed: 293 average time/residue: 0.2448 time to fit residues: 99.4700 Evaluate side-chains 285 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 246 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 39 average time/residue: 0.0979 time to fit residues: 9.1798 ------------------------------------------------------------------------------- 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: 0.0970 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 0.0470 chunk 78 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 147 GLN F 128 ASN F 155 ASN F 185 GLN G 117 GLN O 117 GLN O 147 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 1.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 11247 Z= 0.139 Angle : 0.546 9.342 15262 Z= 0.274 Chirality : 0.039 0.123 1679 Planarity : 0.004 0.037 1936 Dihedral : 4.450 22.047 1456 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer Outliers : 3.30 % 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: 0.53 (0.24), residues: 1296 helix: 1.05 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -2.50 (0.33), residues: 255 *********************** 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 279 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 240 time to evaluate : 1.307 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 39 outliers final: 37 residues processed: 270 average time/residue: 0.2598 time to fit residues: 96.3085 Evaluate side-chains 261 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 37 average time/residue: 0.0982 time to fit residues: 8.7162 ------------------------------------------------------------------------------- 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: 0.8980 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN D 117 GLN E 147 GLN F 128 ASN F 155 ASN O 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 1.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11247 Z= 0.168 Angle : 0.594 11.813 15262 Z= 0.289 Chirality : 0.040 0.187 1679 Planarity : 0.004 0.037 1936 Dihedral : 4.482 24.024 1456 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % 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: 1.05 (0.24), residues: 1296 helix: 1.38 (0.17), residues: 995 sheet: None (None), residues: 0 loop : -1.58 (0.35), residues: 301 *********************** 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 274 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 238 time to evaluate : 1.214 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 36 outliers final: 34 residues processed: 265 average time/residue: 0.2553 time to fit residues: 91.9228 Evaluate side-chains 260 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 226 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 34 average time/residue: 0.0931 time to fit residues: 7.7351 ------------------------------------------------------------------------------- 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: 1.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 101 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN O 117 GLN O 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 1.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11247 Z= 0.162 Angle : 0.588 9.678 15262 Z= 0.286 Chirality : 0.040 0.187 1679 Planarity : 0.004 0.042 1936 Dihedral : 4.474 22.641 1456 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % 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: 1.10 (0.24), residues: 1296 helix: 1.43 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 300 ********************** 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 266 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 1.248 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. outliers start: 33 outliers final: 33 residues processed: 260 average time/residue: 0.2682 time to fit residues: 94.7604 Evaluate side-chains 256 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 223 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 33 average time/residue: 0.0950 time to fit residues: 7.7856 ------------------------------------------------------------------------------- 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: 3.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN O 117 GLN O 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.129039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.118056 restraints weight = 14061.893| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.19 r_work: 0.3127 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 1.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11247 Z= 0.200 Angle : 0.630 12.491 15262 Z= 0.303 Chirality : 0.041 0.194 1679 Planarity : 0.004 0.039 1936 Dihedral : 4.656 24.733 1456 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 2.70 % 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: 1.00 (0.24), residues: 1296 helix: 1.39 (0.17), residues: 995 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 301 =============================================================================== Job complete usr+sys time: 2625.94 seconds wall clock time: 50 minutes 21.29 seconds (3021.29 seconds total)