Starting phenix.real_space_refine on Mon Jun 9 12:13:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1h_8902/06_2025/6n1h_8902.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1h_8902/06_2025/6n1h_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/cci-nas-00/data/ceres_data/6n1h_8902/06_2025/6n1h_8902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1h_8902/06_2025/6n1h_8902.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1h_8902/06_2025/6n1h_8902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1h_8902/06_2025/6n1h_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.31, per 1000 atoms: 0.57 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.2 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: 1.11 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: 2.75 Time building geometry restraints manager: 3.18 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: 71 2.35 - 3.20: 9697 3.20 - 4.05: 28379 4.05 - 4.90: 53795 Warning: very small nonbonded interaction distances. Nonbonded interactions: 91948 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 91943 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: 0.470 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.780 Find NCS groups from input model: 0.440 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.140 ------------------------------------------------------------------------------- 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 : 0.008 0.432 11249 Z= 0.562 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 Details of bonding type rmsd hydrogen bonds : bond 0.28419 ( 528) hydrogen bonds : angle 9.46194 ( 1488) covalent geometry : bond 0.00616 (11247) covalent geometry : angle 1.12862 (15262) Misc. bond : bond 0.36714 ( 2) *********************** 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 to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 2.034 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: 0.2966 time to fit residues: 112.4156 Evaluate side-chains 188 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 K 118 HIS L 145 GLN O 117 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.170413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.155323 restraints weight = 13888.324| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.18 r_work: 0.3619 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11249 Z= 0.145 Angle : 0.659 9.133 15262 Z= 0.345 Chirality : 0.043 0.202 1679 Planarity : 0.007 0.049 1936 Dihedral : 6.865 47.368 1500 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.37 % Allowed : 7.27 % Favored : 90.36 % 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: -3.94 (0.18), residues: 1296 helix: -2.29 (0.13), residues: 993 sheet: None (None), residues: 0 loop : -2.98 (0.26), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 171 HIS 0.007 0.002 HIS G 118 PHE 0.023 0.002 PHE N 163 TYR 0.024 0.002 TYR B 187 ARG 0.020 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.02711 ( 528) hydrogen bonds : angle 5.04869 ( 1488) covalent geometry : bond 0.00340 (11247) covalent geometry : angle 0.65874 (15262) Misc. bond : bond 0.00400 ( 2) *********************** 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 230 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 115 ILE cc_start: 0.7652 (mm) cc_final: 0.7341 (mm) REVERT: H 112 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5453 (tm) REVERT: H 163 PHE cc_start: 0.6014 (m-10) cc_final: 0.5664 (m-80) REVERT: I 139 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6632 (mtmt) REVERT: J 123 ILE cc_start: 0.7363 (mm) cc_final: 0.7005 (mm) REVERT: K 144 GLU cc_start: 0.6902 (tp30) cc_final: 0.6100 (tt0) REVERT: K 159 MET cc_start: 0.7023 (tpt) cc_final: 0.6782 (tpt) outliers start: 28 outliers final: 15 residues processed: 223 average time/residue: 0.2960 time to fit residues: 95.9713 Evaluate side-chains 184 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 172 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 M residue 112 LEU Chi-restraints excluded: chain N residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 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 128 ASN C 155 ASN ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 GLN L 145 GLN N 185 GLN O 117 GLN O 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.169062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.153446 restraints weight = 13924.224| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.23 r_work: 0.3565 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 11249 Z= 0.151 Angle : 0.658 9.581 15262 Z= 0.336 Chirality : 0.041 0.168 1679 Planarity : 0.005 0.037 1936 Dihedral : 5.610 42.421 1468 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.62 % Allowed : 10.82 % 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: -1.88 (0.22), residues: 1296 helix: -0.81 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -2.28 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 131 HIS 0.004 0.001 HIS L 113 PHE 0.024 0.002 PHE D 114 TYR 0.012 0.001 TYR B 187 ARG 0.006 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 528) hydrogen bonds : angle 4.57864 ( 1488) covalent geometry : bond 0.00348 (11247) covalent geometry : angle 0.65799 (15262) Misc. bond : bond 0.00766 ( 2) *********************** 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 290 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7066 (tt) cc_final: 0.6657 (tp) REVERT: B 179 GLN cc_start: 0.5850 (mt0) cc_final: 0.5608 (mt0) REVERT: C 112 LEU cc_start: 0.4787 (OUTLIER) cc_final: 0.4455 (tt) REVERT: C 159 MET cc_start: 0.8773 (mmm) cc_final: 0.8440 (mmm) REVERT: E 113 HIS cc_start: 0.7282 (t-170) cc_final: 0.6894 (t-170) REVERT: E 188 LEU cc_start: 0.7895 (tp) cc_final: 0.7583 (tp) REVERT: G 112 LEU cc_start: 0.3336 (OUTLIER) cc_final: 0.3064 (mp) REVERT: G 134 ASP cc_start: 0.7212 (m-30) cc_final: 0.6768 (m-30) REVERT: G 163 PHE cc_start: 0.8877 (m-10) cc_final: 0.8565 (m-80) REVERT: H 161 LYS cc_start: 0.8479 (tppt) cc_final: 0.8279 (tptp) REVERT: I 139 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: I 157 SER cc_start: 0.8600 (t) cc_final: 0.8379 (m) REVERT: J 112 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5773 (tm) REVERT: J 123 ILE cc_start: 0.8209 (mm) cc_final: 0.7692 (mt) REVERT: J 164 SER cc_start: 0.9131 (t) cc_final: 0.8925 (t) REVERT: K 122 LEU cc_start: 0.8543 (mt) cc_final: 0.8240 (mt) REVERT: M 117 GLN cc_start: 0.7064 (tt0) cc_final: 0.6800 (tt0) REVERT: M 132 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7625 (mt) REVERT: M 190 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7003 (mp0) REVERT: P 142 THR cc_start: 0.7843 (p) cc_final: 0.7580 (p) outliers start: 31 outliers final: 14 residues processed: 280 average time/residue: 0.2564 time to fit residues: 99.0507 Evaluate side-chains 225 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain C residue 133 LEU 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 G residue 112 LEU Chi-restraints excluded: chain G residue 172 THR 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 M residue 112 LEU Chi-restraints excluded: chain M residue 132 LEU 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 12 optimal weight: 0.2980 chunk 94 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 118 HIS C 185 GLN D 147 GLN H 145 GLN O 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.163632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.149082 restraints weight = 13804.076| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.15 r_work: 0.3524 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.8749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11249 Z= 0.114 Angle : 0.573 10.262 15262 Z= 0.294 Chirality : 0.041 0.168 1679 Planarity : 0.004 0.041 1936 Dihedral : 5.346 45.051 1463 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.11 % Allowed : 13.36 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.61 (0.23), residues: 1296 helix: 0.09 (0.17), residues: 994 sheet: None (None), residues: 0 loop : -1.76 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 131 HIS 0.004 0.001 HIS A 118 PHE 0.021 0.002 PHE K 163 TYR 0.016 0.001 TYR I 137 ARG 0.004 0.001 ARG H 160 Details of bonding type rmsd hydrogen bonds : bond 0.02484 ( 528) hydrogen bonds : angle 4.27727 ( 1488) covalent geometry : bond 0.00257 (11247) covalent geometry : angle 0.57328 (15262) Misc. bond : bond 0.00478 ( 2) *********************** 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 273 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 1.293 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 GLN cc_start: 0.6396 (mt0) cc_final: 0.6155 (mt0) REVERT: C 112 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4753 (tt) REVERT: D 159 MET cc_start: 0.8707 (mmm) cc_final: 0.8395 (mmm) REVERT: F 116 ASP cc_start: 0.8099 (m-30) cc_final: 0.7744 (m-30) REVERT: G 134 ASP cc_start: 0.7671 (m-30) cc_final: 0.7286 (m-30) REVERT: H 134 ASP cc_start: 0.7665 (m-30) cc_final: 0.7401 (m-30) REVERT: H 161 LYS cc_start: 0.8941 (tppt) cc_final: 0.8625 (tptp) REVERT: I 137 TYR cc_start: 0.8348 (t80) cc_final: 0.7979 (t80) REVERT: I 194 ARG cc_start: 0.6241 (ttp80) cc_final: 0.5847 (tmt-80) REVERT: J 112 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5695 (tm) REVERT: J 128 ASN cc_start: 0.8364 (t0) cc_final: 0.8162 (t0) REVERT: K 122 LEU cc_start: 0.8945 (mt) cc_final: 0.8538 (mt) REVERT: K 132 LEU cc_start: 0.8600 (mt) cc_final: 0.8373 (mp) REVERT: M 117 GLN cc_start: 0.7445 (tt0) cc_final: 0.7058 (tt0) REVERT: M 190 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7126 (mp0) outliers start: 25 outliers final: 15 residues processed: 264 average time/residue: 0.3010 time to fit residues: 112.0286 Evaluate side-chains 244 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 142 THR 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 154 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 67 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 4 optimal weight: 0.0370 chunk 127 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 overall best weight: 1.3064 ------------------------------------------------------------------------------- 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 E 118 HIS G 155 ASN H 145 GLN ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.144074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.131123 restraints weight = 14079.276| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.14 r_work: 0.3310 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 1.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 11249 Z= 0.166 Angle : 0.691 15.798 15262 Z= 0.349 Chirality : 0.045 0.351 1679 Planarity : 0.005 0.042 1936 Dihedral : 5.599 46.703 1463 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.87 % Allowed : 13.69 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1296 helix: 0.40 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.56 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 169 HIS 0.004 0.001 HIS D 113 PHE 0.017 0.002 PHE A 114 TYR 0.012 0.002 TYR A 146 ARG 0.005 0.001 ARG F 160 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 528) hydrogen bonds : angle 4.68183 ( 1488) covalent geometry : bond 0.00399 (11247) covalent geometry : angle 0.69099 (15262) Misc. bond : bond 0.00571 ( 2) *********************** 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 339 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 1.202 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8443 (m-30) cc_final: 0.8232 (m-30) REVERT: B 164 SER cc_start: 0.7984 (t) cc_final: 0.7671 (p) REVERT: B 183 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7296 (mm-30) REVERT: C 112 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.5970 (tm) REVERT: C 183 GLU cc_start: 0.7268 (mp0) cc_final: 0.7055 (mp0) REVERT: E 117 GLN cc_start: 0.8693 (tt0) cc_final: 0.8446 (tt0) REVERT: E 182 ARG cc_start: 0.8462 (mtt90) cc_final: 0.8212 (mtt-85) REVERT: F 116 ASP cc_start: 0.8331 (m-30) cc_final: 0.8102 (m-30) REVERT: G 134 ASP cc_start: 0.8424 (m-30) cc_final: 0.7933 (m-30) REVERT: G 155 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.7702 (m110) REVERT: H 134 ASP cc_start: 0.8151 (m-30) cc_final: 0.7916 (m-30) REVERT: H 161 LYS cc_start: 0.9236 (tppt) cc_final: 0.8958 (tptm) REVERT: I 117 GLN cc_start: 0.8073 (tt0) cc_final: 0.7859 (tt0) REVERT: I 137 TYR cc_start: 0.8912 (t80) cc_final: 0.8435 (t80) REVERT: I 142 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8761 (m) REVERT: I 176 LEU cc_start: 0.8889 (tt) cc_final: 0.8681 (tp) REVERT: I 194 ARG cc_start: 0.6619 (ttp80) cc_final: 0.6180 (tmt-80) REVERT: J 112 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6759 (tm) REVERT: J 123 ILE cc_start: 0.9102 (mm) cc_final: 0.8900 (mt) REVERT: J 134 ASP cc_start: 0.8894 (m-30) cc_final: 0.8669 (m-30) REVERT: J 139 LYS cc_start: 0.8796 (mttt) cc_final: 0.8424 (mttt) REVERT: K 146 TYR cc_start: 0.9309 (t80) cc_final: 0.8938 (t80) REVERT: K 161 LYS cc_start: 0.8836 (tptp) cc_final: 0.8631 (tppt) REVERT: K 191 ASP cc_start: 0.8299 (t70) cc_final: 0.8039 (t0) REVERT: M 112 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7151 (tm) REVERT: M 175 ASP cc_start: 0.8274 (p0) cc_final: 0.7855 (m-30) REVERT: N 159 MET cc_start: 0.2896 (ppp) cc_final: 0.2285 (tpp) REVERT: N 163 PHE cc_start: 0.8649 (m-80) cc_final: 0.8385 (m-80) outliers start: 34 outliers final: 12 residues processed: 324 average time/residue: 0.2598 time to fit residues: 113.8705 Evaluate side-chains 272 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 255 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 112 LEU 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 155 ASN Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 142 THR 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 154 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 19 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 155 ASN J 118 HIS M 118 HIS O 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.140524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.127995 restraints weight = 14211.850| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.13 r_work: 0.3274 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 1.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11249 Z= 0.122 Angle : 0.599 9.194 15262 Z= 0.302 Chirality : 0.042 0.137 1679 Planarity : 0.004 0.038 1936 Dihedral : 5.290 47.126 1463 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.28 % Allowed : 15.64 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.04 (0.24), residues: 1296 helix: 0.53 (0.17), residues: 993 sheet: None (None), residues: 0 loop : -1.42 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 171 HIS 0.004 0.001 HIS E 113 PHE 0.014 0.001 PHE A 114 TYR 0.011 0.001 TYR I 137 ARG 0.004 0.001 ARG J 160 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 528) hydrogen bonds : angle 4.36121 ( 1488) covalent geometry : bond 0.00294 (11247) covalent geometry : angle 0.59852 (15262) Misc. bond : bond 0.00528 ( 2) *********************** 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 294 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 1.211 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8367 (m-30) cc_final: 0.8133 (m-30) REVERT: B 187 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6793 (p90) REVERT: D 139 LYS cc_start: 0.8219 (mppt) cc_final: 0.7885 (mmtm) REVERT: E 117 GLN cc_start: 0.8638 (tt0) cc_final: 0.8397 (tt0) REVERT: E 182 ARG cc_start: 0.8569 (mtt90) cc_final: 0.8280 (mtt-85) REVERT: F 116 ASP cc_start: 0.8461 (m-30) cc_final: 0.8194 (m-30) REVERT: F 143 ASP cc_start: 0.8302 (t70) cc_final: 0.7906 (t70) REVERT: G 134 ASP cc_start: 0.8408 (m-30) cc_final: 0.7991 (m-30) REVERT: H 146 TYR cc_start: 0.9240 (t80) cc_final: 0.9014 (t80) REVERT: H 161 LYS cc_start: 0.9297 (tppt) cc_final: 0.8972 (tptm) REVERT: I 137 TYR cc_start: 0.8834 (t80) cc_final: 0.8279 (t80) REVERT: I 194 ARG cc_start: 0.6756 (ttp80) cc_final: 0.6329 (tmt-80) REVERT: J 112 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6433 (tm) REVERT: J 139 LYS cc_start: 0.8865 (mttt) cc_final: 0.8588 (mttt) REVERT: J 144 GLU cc_start: 0.7879 (mp0) cc_final: 0.7533 (mp0) REVERT: K 116 ASP cc_start: 0.8544 (m-30) cc_final: 0.8296 (m-30) REVERT: K 146 TYR cc_start: 0.9226 (t80) cc_final: 0.8725 (t80) REVERT: L 183 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7342 (mm-30) REVERT: L 193 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8160 (mt-10) REVERT: M 112 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6869 (tm) REVERT: M 175 ASP cc_start: 0.8312 (p0) cc_final: 0.7941 (m-30) REVERT: O 147 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7507 (pp30) REVERT: P 156 PRO cc_start: 0.9261 (Cg_exo) cc_final: 0.9052 (Cg_endo) outliers start: 27 outliers final: 13 residues processed: 285 average time/residue: 0.2639 time to fit residues: 102.0285 Evaluate side-chains 263 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 115 ILE 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 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 O residue 112 LEU Chi-restraints excluded: chain O residue 147 GLN Chi-restraints excluded: chain P residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 71 optimal weight: 0.0370 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS F 147 GLN G 117 GLN H 147 GLN O 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.124701 restraints weight = 14433.294| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.13 r_work: 0.3229 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 1.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11249 Z= 0.122 Angle : 0.611 9.592 15262 Z= 0.303 Chirality : 0.042 0.162 1679 Planarity : 0.004 0.039 1936 Dihedral : 5.053 48.750 1460 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.20 % Allowed : 16.31 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.06 (0.23), residues: 1296 helix: 0.55 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -2.28 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 131 HIS 0.007 0.001 HIS G 113 PHE 0.014 0.001 PHE A 114 TYR 0.015 0.001 TYR H 137 ARG 0.005 0.001 ARG C 194 Details of bonding type rmsd hydrogen bonds : bond 0.02884 ( 528) hydrogen bonds : angle 4.30781 ( 1488) covalent geometry : bond 0.00296 (11247) covalent geometry : angle 0.61064 (15262) Misc. bond : bond 0.00559 ( 2) *********************** 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 270 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 1.157 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8361 (m-30) cc_final: 0.8153 (m-30) REVERT: B 190 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7201 (mt-10) REVERT: D 139 LYS cc_start: 0.8200 (mppt) cc_final: 0.7911 (mmtm) REVERT: E 117 GLN cc_start: 0.8594 (tt0) cc_final: 0.8330 (tt0) REVERT: E 182 ARG cc_start: 0.8530 (mtt90) cc_final: 0.8247 (mtt-85) REVERT: F 116 ASP cc_start: 0.8505 (m-30) cc_final: 0.8190 (m-30) REVERT: G 134 ASP cc_start: 0.8394 (m-30) cc_final: 0.7870 (m-30) REVERT: H 145 GLN cc_start: 0.9203 (mt0) cc_final: 0.8992 (mt0) REVERT: H 146 TYR cc_start: 0.9265 (t80) cc_final: 0.8989 (t80) REVERT: H 161 LYS cc_start: 0.9317 (tppt) cc_final: 0.8984 (tptm) REVERT: I 194 ARG cc_start: 0.6852 (ttp80) cc_final: 0.6383 (tmt-80) REVERT: J 112 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6489 (tm) REVERT: J 123 ILE cc_start: 0.9100 (mm) cc_final: 0.8804 (mt) REVERT: J 144 GLU cc_start: 0.7861 (mp0) cc_final: 0.7599 (mp0) REVERT: K 134 ASP cc_start: 0.7908 (m-30) cc_final: 0.7434 (m-30) REVERT: L 183 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7348 (mm-30) REVERT: L 193 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8229 (mt-10) REVERT: M 112 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6855 (tm) REVERT: M 175 ASP cc_start: 0.8220 (p0) cc_final: 0.7880 (m-30) REVERT: N 162 LEU cc_start: 0.8452 (tt) cc_final: 0.8203 (tp) REVERT: O 147 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7513 (pp30) outliers start: 26 outliers final: 15 residues processed: 260 average time/residue: 0.2278 time to fit residues: 83.5647 Evaluate side-chains 247 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 166 THR 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 O residue 112 LEU Chi-restraints excluded: chain O residue 147 GLN 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 109 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 chunk 88 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 E 147 GLN G 117 GLN H 147 GLN O 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.136290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.123790 restraints weight = 14214.445| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.22 r_work: 0.3210 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 1.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 11249 Z= 0.115 Angle : 0.604 10.136 15262 Z= 0.298 Chirality : 0.042 0.220 1679 Planarity : 0.004 0.039 1936 Dihedral : 4.985 49.232 1460 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.03 % Allowed : 16.99 % Favored : 80.98 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.61 (0.24), residues: 1296 helix: 0.95 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.005 0.001 HIS C 113 PHE 0.013 0.001 PHE A 114 TYR 0.017 0.001 TYR I 137 ARG 0.004 0.000 ARG N 125 Details of bonding type rmsd hydrogen bonds : bond 0.02753 ( 528) hydrogen bonds : angle 4.23267 ( 1488) covalent geometry : bond 0.00277 (11247) covalent geometry : angle 0.60366 (15262) Misc. bond : bond 0.00606 ( 2) *********************** 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 264 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 1.380 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8297 (m-30) cc_final: 0.8085 (m-30) REVERT: B 183 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7211 (tp30) REVERT: C 112 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5510 (tp) REVERT: D 134 ASP cc_start: 0.8432 (m-30) cc_final: 0.8202 (m-30) REVERT: D 139 LYS cc_start: 0.8139 (mppt) cc_final: 0.7785 (mmtm) REVERT: D 190 GLU cc_start: 0.7098 (mp0) cc_final: 0.6748 (mm-30) REVERT: E 117 GLN cc_start: 0.8628 (tt0) cc_final: 0.8358 (tt0) REVERT: E 165 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: E 182 ARG cc_start: 0.8609 (mtt90) cc_final: 0.8350 (mtt-85) REVERT: F 116 ASP cc_start: 0.8428 (m-30) cc_final: 0.8162 (m-30) REVERT: G 134 ASP cc_start: 0.8417 (m-30) cc_final: 0.7922 (m-30) REVERT: H 134 ASP cc_start: 0.7959 (m-30) cc_final: 0.7701 (m-30) REVERT: H 145 GLN cc_start: 0.9200 (mt0) cc_final: 0.8988 (mt0) REVERT: H 146 TYR cc_start: 0.9177 (t80) cc_final: 0.8915 (t80) REVERT: H 161 LYS cc_start: 0.9328 (tppt) cc_final: 0.9027 (tptm) REVERT: I 194 ARG cc_start: 0.6891 (ttp80) cc_final: 0.6399 (tmt-80) REVERT: J 123 ILE cc_start: 0.9143 (mm) cc_final: 0.8790 (mt) REVERT: K 134 ASP cc_start: 0.7996 (m-30) cc_final: 0.7448 (m-30) REVERT: L 182 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8011 (mtm-85) REVERT: L 193 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8244 (mt-10) REVERT: M 112 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6967 (tm) REVERT: N 162 LEU cc_start: 0.8772 (tt) cc_final: 0.8515 (tp) REVERT: O 144 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7655 (tt0) REVERT: O 147 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8173 (pm20) outliers start: 24 outliers final: 13 residues processed: 256 average time/residue: 0.2809 time to fit residues: 102.3659 Evaluate side-chains 251 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 165 PHE 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 M residue 112 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 147 GLN 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 76 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 G 117 GLN H 147 GLN O 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.133504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121681 restraints weight = 14301.616| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.13 r_work: 0.3262 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 1.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11249 Z= 0.121 Angle : 0.613 9.715 15262 Z= 0.301 Chirality : 0.042 0.203 1679 Planarity : 0.004 0.039 1936 Dihedral : 4.816 37.887 1458 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.69 % Allowed : 16.91 % Favored : 81.40 % 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: 0.27 (0.24), residues: 1296 helix: 0.80 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -2.20 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP N 131 HIS 0.005 0.001 HIS E 113 PHE 0.015 0.001 PHE M 114 TYR 0.017 0.001 TYR I 137 ARG 0.004 0.001 ARG P 194 Details of bonding type rmsd hydrogen bonds : bond 0.02875 ( 528) hydrogen bonds : angle 4.22211 ( 1488) covalent geometry : bond 0.00297 (11247) covalent geometry : angle 0.61251 (15262) Misc. bond : bond 0.00576 ( 2) *********************** 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 269 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 1.211 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 183 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7478 (tp30) REVERT: D 139 LYS cc_start: 0.8177 (mppt) cc_final: 0.7873 (mmtm) REVERT: D 190 GLU cc_start: 0.7254 (mp0) cc_final: 0.6897 (mm-30) REVERT: E 117 GLN cc_start: 0.8605 (tt0) cc_final: 0.8349 (tt0) REVERT: E 165 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: E 182 ARG cc_start: 0.8700 (mtt90) cc_final: 0.8456 (mtt-85) REVERT: F 116 ASP cc_start: 0.8634 (m-30) cc_final: 0.8410 (m-30) REVERT: G 134 ASP cc_start: 0.8379 (m-30) cc_final: 0.7919 (m-30) REVERT: H 146 TYR cc_start: 0.9151 (t80) cc_final: 0.8861 (t80) REVERT: H 161 LYS cc_start: 0.9301 (tppt) cc_final: 0.9020 (tptm) REVERT: I 112 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6438 (tp) REVERT: I 194 ARG cc_start: 0.7034 (ttp80) cc_final: 0.6465 (tmt-80) REVERT: J 123 ILE cc_start: 0.9208 (mm) cc_final: 0.8883 (mt) REVERT: K 134 ASP cc_start: 0.8017 (m-30) cc_final: 0.7484 (m-30) REVERT: K 146 TYR cc_start: 0.9362 (t80) cc_final: 0.9129 (t80) REVERT: K 164 SER cc_start: 0.8911 (t) cc_final: 0.8421 (m) REVERT: L 116 ASP cc_start: 0.8457 (m-30) cc_final: 0.8192 (m-30) REVERT: L 182 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.8269 (mtm-85) REVERT: N 128 ASN cc_start: 0.7895 (t0) cc_final: 0.7404 (t0) REVERT: N 155 ASN cc_start: 0.8602 (t0) cc_final: 0.8355 (m-40) REVERT: O 144 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7692 (tt0) REVERT: O 147 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7576 (pp30) REVERT: P 147 GLN cc_start: 0.8898 (mt0) cc_final: 0.8586 (pt0) outliers start: 20 outliers final: 11 residues processed: 262 average time/residue: 0.2479 time to fit residues: 89.4164 Evaluate side-chains 252 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 154 THR 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 J residue 154 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 147 GLN 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 21 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS G 117 GLN H 145 GLN H 147 GLN O 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.133649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.121751 restraints weight = 14140.791| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.20 r_work: 0.3186 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 1.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11249 Z= 0.119 Angle : 0.648 13.475 15262 Z= 0.309 Chirality : 0.042 0.211 1679 Planarity : 0.004 0.040 1936 Dihedral : 4.687 28.002 1456 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.52 % Allowed : 18.09 % Favored : 80.39 % 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: 0.71 (0.24), residues: 1296 helix: 1.05 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 131 HIS 0.005 0.001 HIS E 113 PHE 0.015 0.001 PHE M 114 TYR 0.017 0.001 TYR I 137 ARG 0.010 0.001 ARG G 194 Details of bonding type rmsd hydrogen bonds : bond 0.02860 ( 528) hydrogen bonds : angle 4.21679 ( 1488) covalent geometry : bond 0.00289 (11247) covalent geometry : angle 0.64761 (15262) Misc. bond : bond 0.00562 ( 2) ********************** 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 251 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 1.191 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. REVERT: D 139 LYS cc_start: 0.8203 (mppt) cc_final: 0.7834 (mmtm) REVERT: D 190 GLU cc_start: 0.7204 (mp0) cc_final: 0.6799 (mm-30) REVERT: E 117 GLN cc_start: 0.8547 (tt0) cc_final: 0.8265 (tt0) REVERT: E 165 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: E 182 ARG cc_start: 0.8704 (mtt90) cc_final: 0.8473 (mtt-85) REVERT: G 134 ASP cc_start: 0.8432 (m-30) cc_final: 0.8014 (m-30) REVERT: G 194 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6775 (ttp80) REVERT: H 146 TYR cc_start: 0.9206 (t80) cc_final: 0.8885 (t80) REVERT: H 161 LYS cc_start: 0.9302 (tppt) cc_final: 0.9025 (tptm) REVERT: I 141 LEU cc_start: 0.8610 (mp) cc_final: 0.8395 (mt) REVERT: I 194 ARG cc_start: 0.6926 (ttp80) cc_final: 0.6345 (tmt-80) REVERT: J 123 ILE cc_start: 0.9197 (mm) cc_final: 0.8870 (mt) REVERT: K 134 ASP cc_start: 0.7982 (m-30) cc_final: 0.7522 (m-30) REVERT: K 146 TYR cc_start: 0.9374 (t80) cc_final: 0.9109 (t80) REVERT: L 116 ASP cc_start: 0.8484 (m-30) cc_final: 0.8247 (m-30) REVERT: L 182 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8045 (mtm-85) REVERT: N 155 ASN cc_start: 0.8644 (t0) cc_final: 0.8319 (t0) REVERT: N 159 MET cc_start: 0.8465 (tpp) cc_final: 0.8248 (tpt) REVERT: O 147 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7578 (pp30) outliers start: 18 outliers final: 13 residues processed: 245 average time/residue: 0.2487 time to fit residues: 83.6598 Evaluate side-chains 243 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 154 THR 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 J residue 154 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 147 GLN 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 56 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 0.0470 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 0.0170 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.136284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.124358 restraints weight = 14036.749| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.17 r_work: 0.3247 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 1.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 11249 Z= 0.104 Angle : 0.620 12.060 15262 Z= 0.298 Chirality : 0.041 0.180 1679 Planarity : 0.004 0.039 1936 Dihedral : 4.575 26.546 1456 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.52 % Allowed : 17.92 % Favored : 80.56 % 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: 0.87 (0.24), residues: 1296 helix: 1.15 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.25 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP N 131 HIS 0.005 0.001 HIS E 113 PHE 0.014 0.001 PHE M 114 TYR 0.015 0.001 TYR I 137 ARG 0.009 0.000 ARG G 194 Details of bonding type rmsd hydrogen bonds : bond 0.02621 ( 528) hydrogen bonds : angle 4.10291 ( 1488) covalent geometry : bond 0.00238 (11247) covalent geometry : angle 0.62000 (15262) Misc. bond : bond 0.00510 ( 2) =============================================================================== Job complete usr+sys time: 5503.45 seconds wall clock time: 96 minutes 39.02 seconds (5799.02 seconds total)