Starting phenix.real_space_refine on Wed Sep 25 14:56:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/09_2024/6n1h_8902.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/09_2024/6n1h_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_8902/09_2024/6n1h_8902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/09_2024/6n1h_8902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/09_2024/6n1h_8902.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1h_8902/09_2024/6n1h_8902.cif" } 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. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.55, 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 - 3.00 Amino acid : True - 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: 2.80 Conformation dependent library (CDL) restraints added in 1.4 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: 1.23 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: 2.69 Time building geometry restraints manager: 3.28 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: 0.00 - 2.15: 14511 2.15 - 4.30: 576 4.30 - 6.44: 126 6.44 - 8.59: 33 8.59 - 10.74: 16 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 3.120 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 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.510 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.870 Find NCS groups from input model: 0.480 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.070 ------------------------------------------------------------------------------- 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 % Allowed : 2.96 % Favored : 93.07 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP N 131 HIS 0.003 0.001 HIS F 118 PHE 0.021 0.004 PHE K 163 TYR 0.006 0.002 TYR K 146 ARG 0.010 0.002 ARG A 125 *********************** 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 : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 115 ILE cc_start: 0.5331 (mm) cc_final: 0.4946 (mm) REVERT: L 112 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6136 (tm) REVERT: O 154 THR cc_start: 0.7194 (p) cc_final: 0.6895 (m) outliers start: 47 outliers final: 37 residues processed: 264 average time/residue: 0.2269 time to fit residues: 84.2875 Evaluate side-chains 188 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 172 THR 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: 0.8980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 HIS J 118 HIS K 118 HIS L 145 GLN O 117 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11247 Z= 0.217 Angle : 0.675 9.591 15262 Z= 0.350 Chirality : 0.043 0.172 1679 Planarity : 0.007 0.051 1936 Dihedral : 6.766 47.293 1500 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.28 % Allowed : 7.44 % Favored : 90.28 % 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: -3.90 (0.18), residues: 1296 helix: -2.25 (0.13), residues: 993 sheet: None (None), residues: 0 loop : -3.03 (0.26), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 171 HIS 0.005 0.001 HIS G 118 PHE 0.022 0.002 PHE H 114 TYR 0.017 0.002 TYR B 187 ARG 0.010 0.001 ARG E 160 *********************** 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 231 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 115 ILE cc_start: 0.7623 (mm) cc_final: 0.7342 (mm) REVERT: H 112 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.5223 (tm) REVERT: H 163 PHE cc_start: 0.5931 (m-10) cc_final: 0.5505 (m-80) REVERT: I 139 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6533 (mtmt) REVERT: J 123 ILE cc_start: 0.7348 (mm) cc_final: 0.6996 (mm) REVERT: K 144 GLU cc_start: 0.6538 (tp30) cc_final: 0.5977 (tt0) REVERT: K 159 MET cc_start: 0.6940 (tpt) cc_final: 0.6725 (tpt) REVERT: O 146 TYR cc_start: 0.6846 (t80) cc_final: 0.6500 (t80) outliers start: 27 outliers final: 15 residues processed: 222 average time/residue: 0.2235 time to fit residues: 70.3696 Evaluate side-chains 184 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain M residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 155 ASN C 185 GLN ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN ** J 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN L 155 ASN N 185 GLN O 117 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.8289 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= 0.254 Angle : 0.723 11.105 15262 Z= 0.366 Chirality : 0.043 0.215 1679 Planarity : 0.006 0.046 1936 Dihedral : 5.653 43.005 1466 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.87 % Allowed : 10.57 % Favored : 86.56 % 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: -1.54 (0.22), residues: 1296 helix: -0.76 (0.16), residues: 918 sheet: None (None), residues: 0 loop : -1.28 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 171 HIS 0.005 0.001 HIS C 113 PHE 0.022 0.002 PHE D 114 TYR 0.015 0.001 TYR B 187 ARG 0.006 0.001 ARG F 160 *********************** 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 300 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 266 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 123 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7516 (mm) REVERT: D 112 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.4221 (tm) REVERT: D 159 MET cc_start: 0.8136 (mmm) cc_final: 0.7743 (mmm) REVERT: E 113 HIS cc_start: 0.7352 (t-170) cc_final: 0.7137 (t-170) REVERT: E 159 MET cc_start: 0.8745 (tpt) cc_final: 0.8487 (tpt) REVERT: E 188 LEU cc_start: 0.7973 (tp) cc_final: 0.7729 (tp) REVERT: F 139 LYS cc_start: 0.8352 (mppt) cc_final: 0.8139 (mtmm) REVERT: G 134 ASP cc_start: 0.7563 (m-30) cc_final: 0.7028 (m-30) REVERT: H 161 LYS cc_start: 0.8785 (tppt) cc_final: 0.8532 (tptp) REVERT: I 139 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (mttt) REVERT: I 157 SER cc_start: 0.8681 (t) cc_final: 0.8410 (m) REVERT: J 112 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5726 (tm) REVERT: J 123 ILE cc_start: 0.8353 (mm) cc_final: 0.7836 (mt) REVERT: M 117 GLN cc_start: 0.7283 (tt0) cc_final: 0.6943 (tt0) REVERT: M 132 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8109 (mt) REVERT: M 190 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6871 (mp0) outliers start: 34 outliers final: 17 residues processed: 289 average time/residue: 0.2477 time to fit residues: 98.1112 Evaluate side-chains 234 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain P residue 154 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C 128 ASN G 117 GLN H 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 1.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11247 Z= 0.228 Angle : 0.664 11.028 15262 Z= 0.336 Chirality : 0.044 0.195 1679 Planarity : 0.005 0.045 1936 Dihedral : 5.532 45.886 1464 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.70 % Allowed : 12.93 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1296 helix: -0.09 (0.17), residues: 889 sheet: None (None), residues: 0 loop : -1.59 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 131 HIS 0.006 0.001 HIS C 113 PHE 0.015 0.002 PHE A 114 TYR 0.018 0.002 TYR L 146 ARG 0.009 0.001 ARG B 125 *********************** 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 342 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 1.375 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 159 MET cc_start: 0.8696 (mmm) cc_final: 0.8394 (mmm) REVERT: E 117 GLN cc_start: 0.8527 (tt0) cc_final: 0.8322 (tt0) REVERT: E 182 ARG cc_start: 0.8238 (mtt90) cc_final: 0.8020 (mtt-85) REVERT: G 134 ASP cc_start: 0.8179 (m-30) cc_final: 0.7759 (m-30) REVERT: H 145 GLN cc_start: 0.8993 (mt0) cc_final: 0.8684 (mt0) REVERT: H 161 LYS cc_start: 0.9254 (tppt) cc_final: 0.8871 (tptp) REVERT: J 112 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.5997 (tm) REVERT: J 139 LYS cc_start: 0.8674 (mttt) cc_final: 0.8439 (mttt) REVERT: K 164 SER cc_start: 0.8728 (t) cc_final: 0.8406 (m) REVERT: K 184 SER cc_start: 0.8672 (t) cc_final: 0.8400 (t) REVERT: L 161 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9032 (tppt) REVERT: L 193 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8027 (mt-10) REVERT: M 176 LEU cc_start: 0.8387 (tt) cc_final: 0.7737 (mt) REVERT: M 187 TYR cc_start: 0.8029 (p90) cc_final: 0.7754 (p90) REVERT: M 190 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7098 (mp0) outliers start: 32 outliers final: 13 residues processed: 331 average time/residue: 0.2587 time to fit residues: 115.3501 Evaluate side-chains 267 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 161 LYS Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain P residue 154 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.0020 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN K 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 1.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11247 Z= 0.188 Angle : 0.610 9.066 15262 Z= 0.306 Chirality : 0.042 0.132 1679 Planarity : 0.004 0.042 1936 Dihedral : 5.236 51.505 1463 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.20 % Allowed : 14.88 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1296 helix: 0.22 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 131 HIS 0.005 0.001 HIS E 113 PHE 0.017 0.001 PHE A 114 TYR 0.019 0.001 TYR L 146 ARG 0.006 0.001 ARG B 160 *********************** 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 293 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 267 time to evaluate : 1.330 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 163 PHE cc_start: 0.6940 (m-80) cc_final: 0.6734 (m-80) REVERT: B 190 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6980 (mt-10) REVERT: D 143 ASP cc_start: 0.8274 (t0) cc_final: 0.8012 (t70) REVERT: D 159 MET cc_start: 0.8744 (mmm) cc_final: 0.8465 (mmm) REVERT: E 117 GLN cc_start: 0.8508 (tt0) cc_final: 0.8279 (tt0) REVERT: E 159 MET cc_start: 0.8892 (mmm) cc_final: 0.8570 (mmm) REVERT: E 182 ARG cc_start: 0.8280 (mtt90) cc_final: 0.8043 (mtt-85) REVERT: G 134 ASP cc_start: 0.8309 (m-30) cc_final: 0.7928 (m-30) REVERT: G 147 GLN cc_start: 0.8595 (mt0) cc_final: 0.8352 (mt0) REVERT: H 161 LYS cc_start: 0.9259 (tppt) cc_final: 0.8879 (tptm) REVERT: J 115 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8415 (mm) REVERT: K 134 ASP cc_start: 0.7536 (m-30) cc_final: 0.7257 (m-30) REVERT: K 164 SER cc_start: 0.8690 (t) cc_final: 0.8377 (m) REVERT: K 184 SER cc_start: 0.8687 (t) cc_final: 0.8480 (t) REVERT: L 161 LYS cc_start: 0.9269 (tptm) cc_final: 0.8868 (tppt) REVERT: M 176 LEU cc_start: 0.8444 (tt) cc_final: 0.8116 (mt) REVERT: P 156 PRO cc_start: 0.9150 (Cg_exo) cc_final: 0.8869 (Cg_endo) outliers start: 26 outliers final: 14 residues processed: 282 average time/residue: 0.2591 time to fit residues: 100.1486 Evaluate side-chains 258 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 243 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 147 GLN Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain P residue 154 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 GLN H 147 GLN N 118 HIS O 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 1.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11247 Z= 0.296 Angle : 0.715 13.664 15262 Z= 0.353 Chirality : 0.046 0.265 1679 Planarity : 0.005 0.045 1936 Dihedral : 5.614 46.062 1460 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.37 % Allowed : 15.55 % Favored : 82.08 % 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: -0.67 (0.23), residues: 1296 helix: 0.14 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -2.52 (0.31), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 131 HIS 0.008 0.001 HIS J 113 PHE 0.016 0.002 PHE A 114 TYR 0.021 0.002 TYR L 146 ARG 0.005 0.001 ARG N 125 *********************** 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 309 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 281 time to evaluate : 1.171 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 184 SER cc_start: 0.8924 (t) cc_final: 0.8625 (p) REVERT: D 137 TYR cc_start: 0.8986 (t80) cc_final: 0.8321 (t80) REVERT: D 139 LYS cc_start: 0.8204 (mppt) cc_final: 0.7731 (mmtm) REVERT: D 143 ASP cc_start: 0.8338 (t0) cc_final: 0.7958 (t70) REVERT: D 159 MET cc_start: 0.8758 (mmm) cc_final: 0.8346 (mmm) REVERT: E 117 GLN cc_start: 0.8448 (tt0) cc_final: 0.8124 (tt0) REVERT: E 145 GLN cc_start: 0.9043 (mt0) cc_final: 0.8808 (mt0) REVERT: F 186 SER cc_start: 0.7838 (t) cc_final: 0.7444 (p) REVERT: G 134 ASP cc_start: 0.8333 (m-30) cc_final: 0.7941 (m-30) REVERT: G 143 ASP cc_start: 0.7896 (t0) cc_final: 0.7680 (t70) REVERT: G 147 GLN cc_start: 0.8720 (mt0) cc_final: 0.8479 (mt0) REVERT: H 145 GLN cc_start: 0.9059 (mt0) cc_final: 0.8751 (mt0) REVERT: H 161 LYS cc_start: 0.9284 (tppt) cc_final: 0.8942 (tptm) REVERT: J 112 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5819 (tt) REVERT: J 144 GLU cc_start: 0.7472 (mp0) cc_final: 0.7163 (mp0) REVERT: K 164 SER cc_start: 0.8714 (t) cc_final: 0.8364 (m) REVERT: L 147 GLN cc_start: 0.8831 (mt0) cc_final: 0.8602 (mt0) REVERT: L 182 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7791 (mtm-85) REVERT: N 159 MET cc_start: 0.8210 (mmm) cc_final: 0.7963 (tpt) outliers start: 28 outliers final: 16 residues processed: 301 average time/residue: 0.2603 time to fit residues: 106.0803 Evaluate side-chains 275 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 258 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 143 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 76 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN E 113 HIS F 185 GLN G 117 GLN G 128 ASN H 118 HIS H 147 GLN I 113 HIS M 118 HIS O 117 GLN O 179 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 1.3749 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= 0.162 Angle : 0.605 10.505 15262 Z= 0.301 Chirality : 0.042 0.173 1679 Planarity : 0.004 0.045 1936 Dihedral : 5.140 44.646 1460 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.94 % Allowed : 16.74 % Favored : 81.32 % 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: -0.17 (0.23), residues: 1296 helix: 0.49 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -2.39 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 131 HIS 0.004 0.001 HIS E 113 PHE 0.014 0.001 PHE H 114 TYR 0.023 0.001 TYR I 137 ARG 0.004 0.001 ARG N 125 *********************** 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 292 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 269 time to evaluate : 1.255 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 184 SER cc_start: 0.8809 (t) cc_final: 0.8527 (p) REVERT: D 139 LYS cc_start: 0.8161 (mppt) cc_final: 0.7812 (mmtm) REVERT: D 159 MET cc_start: 0.8806 (mmm) cc_final: 0.8407 (mmm) REVERT: E 117 GLN cc_start: 0.8396 (tt0) cc_final: 0.8055 (tt0) REVERT: F 112 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6747 (tm) REVERT: F 143 ASP cc_start: 0.7727 (t70) cc_final: 0.7435 (t70) REVERT: G 134 ASP cc_start: 0.8318 (m-30) cc_final: 0.7923 (m-30) REVERT: G 143 ASP cc_start: 0.7765 (t0) cc_final: 0.7503 (t70) REVERT: H 161 LYS cc_start: 0.9235 (tppt) cc_final: 0.8926 (tptm) REVERT: H 176 LEU cc_start: 0.8652 (tt) cc_final: 0.8433 (tp) REVERT: J 144 GLU cc_start: 0.7409 (mp0) cc_final: 0.7208 (mp0) REVERT: K 134 ASP cc_start: 0.7534 (m-30) cc_final: 0.7266 (m-30) REVERT: L 182 ARG cc_start: 0.8289 (mtt90) cc_final: 0.7812 (mtm-85) REVERT: L 183 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6953 (mt-10) REVERT: M 182 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8034 (mtt-85) REVERT: N 128 ASN cc_start: 0.7521 (t0) cc_final: 0.7298 (t0) REVERT: N 159 MET cc_start: 0.8227 (mmm) cc_final: 0.8024 (tpp) REVERT: P 182 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7821 (mtt-85) outliers start: 23 outliers final: 16 residues processed: 283 average time/residue: 0.2687 time to fit residues: 102.0941 Evaluate side-chains 268 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 251 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 154 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 37 optimal weight: 0.0020 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 118 HIS E 113 HIS F 145 GLN G 117 GLN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 117 GLN O 117 GLN O 147 GLN O 179 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 1.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11247 Z= 0.168 Angle : 0.629 12.208 15262 Z= 0.305 Chirality : 0.042 0.204 1679 Planarity : 0.004 0.044 1936 Dihedral : 4.905 44.770 1458 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.61 % Allowed : 18.09 % Favored : 80.30 % 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: 0.07 (0.23), residues: 1296 helix: 0.67 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -2.33 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 131 HIS 0.005 0.001 HIS E 113 PHE 0.015 0.001 PHE L 114 TYR 0.024 0.001 TYR I 137 ARG 0.007 0.001 ARG E 182 *********************** 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 267 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 248 time to evaluate : 1.189 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8103 (m-30) cc_final: 0.7837 (m-30) REVERT: B 184 SER cc_start: 0.8773 (t) cc_final: 0.8514 (p) REVERT: D 139 LYS cc_start: 0.8151 (mppt) cc_final: 0.7785 (mmtm) REVERT: D 159 MET cc_start: 0.8804 (mmm) cc_final: 0.8410 (mmm) REVERT: D 190 GLU cc_start: 0.7710 (pp20) cc_final: 0.7313 (mp0) REVERT: E 117 GLN cc_start: 0.8373 (tt0) cc_final: 0.8043 (tt0) REVERT: F 112 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6645 (tm) REVERT: G 134 ASP cc_start: 0.8325 (m-30) cc_final: 0.7936 (m-30) REVERT: G 147 GLN cc_start: 0.8615 (mt0) cc_final: 0.8409 (pt0) REVERT: G 194 ARG cc_start: 0.6922 (ttp80) cc_final: 0.6518 (ttp80) REVERT: H 161 LYS cc_start: 0.9277 (tppt) cc_final: 0.8976 (tptm) REVERT: H 176 LEU cc_start: 0.8700 (tt) cc_final: 0.8391 (tp) REVERT: K 134 ASP cc_start: 0.7486 (m-30) cc_final: 0.7189 (m-30) REVERT: M 182 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8313 (mtm-85) REVERT: N 122 LEU cc_start: 0.5341 (tt) cc_final: 0.5127 (tp) REVERT: N 128 ASN cc_start: 0.7759 (t0) cc_final: 0.7506 (t0) REVERT: P 182 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7797 (mtt-85) outliers start: 19 outliers final: 16 residues processed: 258 average time/residue: 0.2566 time to fit residues: 89.9647 Evaluate side-chains 252 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 235 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 154 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 90 optimal weight: 0.0040 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.9172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 117 GLN O 117 GLN O 179 GLN P 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 1.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11247 Z= 0.184 Angle : 0.630 11.284 15262 Z= 0.306 Chirality : 0.042 0.183 1679 Planarity : 0.004 0.044 1936 Dihedral : 4.863 44.816 1458 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.27 % Allowed : 19.19 % Favored : 79.54 % 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: 0.26 (0.23), residues: 1296 helix: 0.81 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.34 (0.31), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 169 HIS 0.007 0.001 HIS G 113 PHE 0.016 0.001 PHE M 114 TYR 0.024 0.001 TYR I 137 ARG 0.007 0.001 ARG E 182 *********************** 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 257 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 242 time to evaluate : 1.278 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8115 (m-30) cc_final: 0.7701 (m-30) REVERT: B 184 SER cc_start: 0.8696 (t) cc_final: 0.8456 (p) REVERT: D 159 MET cc_start: 0.8811 (mmm) cc_final: 0.8413 (mmm) REVERT: D 190 GLU cc_start: 0.7792 (pp20) cc_final: 0.7402 (mp0) REVERT: E 117 GLN cc_start: 0.8351 (tt0) cc_final: 0.8010 (tt0) REVERT: F 112 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6762 (tm) REVERT: G 134 ASP cc_start: 0.8348 (m-30) cc_final: 0.7947 (m-30) REVERT: G 147 GLN cc_start: 0.8594 (mt0) cc_final: 0.8373 (pt0) REVERT: G 194 ARG cc_start: 0.6896 (ttp80) cc_final: 0.6479 (ttp80) REVERT: H 161 LYS cc_start: 0.9273 (tppt) cc_final: 0.8975 (tptm) REVERT: H 176 LEU cc_start: 0.8635 (tt) cc_final: 0.8381 (tp) REVERT: K 134 ASP cc_start: 0.7055 (m-30) cc_final: 0.6828 (m-30) REVERT: L 182 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7833 (mtm-85) REVERT: M 182 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8312 (mtm-85) REVERT: N 128 ASN cc_start: 0.8169 (t0) cc_final: 0.7855 (t0) REVERT: P 182 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7847 (mtt-85) outliers start: 15 outliers final: 14 residues processed: 248 average time/residue: 0.2674 time to fit residues: 89.4458 Evaluate side-chains 248 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 154 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS G 117 GLN G 128 ASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 117 GLN O 117 GLN O 179 GLN P 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 1.4131 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= 0.165 Angle : 0.610 10.760 15262 Z= 0.298 Chirality : 0.042 0.165 1679 Planarity : 0.004 0.044 1936 Dihedral : 4.778 44.406 1458 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.27 % Allowed : 19.36 % Favored : 79.37 % 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: 0.41 (0.24), residues: 1296 helix: 0.92 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.30 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 131 HIS 0.008 0.001 HIS E 113 PHE 0.019 0.001 PHE M 114 TYR 0.022 0.001 TYR I 137 ARG 0.010 0.001 ARG P 194 ********************** 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 263 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 248 time to evaluate : 1.286 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8208 (m-30) cc_final: 0.7952 (m-30) REVERT: A 194 ARG cc_start: 0.6131 (ttp80) cc_final: 0.5758 (ttp80) REVERT: B 184 SER cc_start: 0.8719 (t) cc_final: 0.8479 (p) REVERT: D 159 MET cc_start: 0.8855 (mmm) cc_final: 0.8482 (mmm) REVERT: D 190 GLU cc_start: 0.7767 (pp20) cc_final: 0.7371 (mp0) REVERT: E 117 GLN cc_start: 0.8298 (tt0) cc_final: 0.7984 (tt0) REVERT: F 112 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6501 (tm) REVERT: G 134 ASP cc_start: 0.8351 (m-30) cc_final: 0.7940 (m-30) REVERT: G 147 GLN cc_start: 0.8560 (mt0) cc_final: 0.8337 (pt0) REVERT: H 134 ASP cc_start: 0.7750 (m-30) cc_final: 0.7471 (m-30) REVERT: H 161 LYS cc_start: 0.9279 (tppt) cc_final: 0.8975 (tptm) REVERT: H 174 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8518 (mtmt) REVERT: H 176 LEU cc_start: 0.8643 (tt) cc_final: 0.8374 (tp) REVERT: L 182 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8021 (mtm-85) REVERT: M 176 LEU cc_start: 0.8519 (tt) cc_final: 0.7801 (mt) REVERT: M 182 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8312 (ttm-80) REVERT: P 182 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.7859 (mtt-85) outliers start: 15 outliers final: 13 residues processed: 254 average time/residue: 0.2689 time to fit residues: 91.7990 Evaluate side-chains 250 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain M residue 175 ASP Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 154 THR 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: 0.4980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 117 GLN O 117 GLN O 179 GLN P 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.129118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.117897 restraints weight = 14036.620| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.19 r_work: 0.3133 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 1.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 11247 Z= 0.203 Angle : 1.127 59.197 15262 Z= 0.638 Chirality : 0.046 0.732 1679 Planarity : 0.005 0.046 1936 Dihedral : 4.833 44.411 1458 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.18 % Allowed : 19.36 % Favored : 79.46 % Cbeta Deviations : 0.08 % 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: 0.41 (0.24), residues: 1296 helix: 0.92 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.30 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 171 HIS 0.007 0.001 HIS E 113 PHE 0.018 0.001 PHE M 114 TYR 0.021 0.001 TYR I 137 ARG 0.014 0.001 ARG F 194 =============================================================================== Job complete usr+sys time: 2651.95 seconds wall clock time: 47 minutes 35.32 seconds (2855.32 seconds total)