Starting phenix.real_space_refine on Fri Feb 14 19:44:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1h_8902/02_2025/6n1h_8902.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1h_8902/02_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_8902/02_2025/6n1h_8902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1h_8902/02_2025/6n1h_8902.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1h_8902/02_2025/6n1h_8902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1h_8902/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.48, per 1000 atoms: 0.59 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: 2.95 Conformation dependent library (CDL) restraints added in 1.1 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: 1.10 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: 2.80 Time building geometry restraints manager: 3.36 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.940 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11247 Z= 0.388 Angle : 1.129 10.738 15262 Z= 0.652 Chirality : 0.058 0.271 1679 Planarity : 0.008 0.062 1936 Dihedral : 12.227 71.692 4143 Min Nonbonded Distance : 0.657 Molprobity Statistics. All-atom Clashscore : 32.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.97 % Allowed : 2.96 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.22 (0.10), residues: 1296 helix: -4.65 (0.05), residues: 976 sheet: None (None), residues: 0 loop : -4.20 (0.22), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP N 131 HIS 0.003 0.001 HIS F 118 PHE 0.021 0.004 PHE K 163 TYR 0.006 0.002 TYR K 146 ARG 0.010 0.002 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 1.103 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: 0.2277 time to fit residues: 84.3610 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 : 1.171 ------------------------------------------------------------------------------- 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 = 13888.329| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.18 r_work: 0.3618 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 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 11247 Z= 0.218 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 : 8.16 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 *********************** 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 : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 115 ILE cc_start: 0.7648 (mm) cc_final: 0.7339 (mm) REVERT: H 112 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5455 (tm) REVERT: H 163 PHE cc_start: 0.6013 (m-10) cc_final: 0.5663 (m-80) REVERT: I 139 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6629 (mtmt) REVERT: J 123 ILE cc_start: 0.7364 (mm) cc_final: 0.7005 (mm) REVERT: K 144 GLU cc_start: 0.6897 (tp30) cc_final: 0.6097 (tt0) REVERT: K 159 MET cc_start: 0.7020 (tpt) cc_final: 0.6780 (tpt) outliers start: 28 outliers final: 15 residues processed: 223 average time/residue: 0.2279 time to fit residues: 72.0983 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 : 1.231 ------------------------------------------------------------------------------- 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: 0.9990 chunk 84 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 chunk 105 optimal weight: 0.0170 chunk 58 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 GLN L 145 GLN O 117 GLN O 147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.170313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.154571 restraints weight = 13947.104| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.23 r_work: 0.3577 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 11247 Z= 0.180 Angle : 0.600 8.865 15262 Z= 0.309 Chirality : 0.040 0.132 1679 Planarity : 0.005 0.041 1936 Dihedral : 5.518 43.000 1468 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.11 % Allowed : 10.57 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1296 helix: -0.76 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 171 HIS 0.005 0.001 HIS L 113 PHE 0.021 0.001 PHE D 114 TYR 0.011 0.001 TYR B 187 ARG 0.005 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 LEU cc_start: 0.4476 (OUTLIER) cc_final: 0.4238 (tt) REVERT: E 188 LEU cc_start: 0.7651 (tp) cc_final: 0.7358 (tp) REVERT: I 112 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7601 (mm) REVERT: I 139 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7687 (mttt) REVERT: J 123 ILE cc_start: 0.7631 (mm) cc_final: 0.7328 (mm) REVERT: K 144 GLU cc_start: 0.6826 (tp30) cc_final: 0.6609 (tt0) REVERT: M 190 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6632 (mp0) outliers start: 25 outliers final: 11 residues processed: 236 average time/residue: 0.2445 time to fit residues: 80.4308 Evaluate side-chains 195 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 112 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 I 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 M residue 112 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: 0.0070 chunk 94 optimal weight: 0.0040 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 45 optimal weight: 0.0040 chunk 80 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN K 155 ASN O 117 GLN O 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.173196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.158088 restraints weight = 13691.086| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.14 r_work: 0.3660 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11247 Z= 0.130 Angle : 0.545 10.567 15262 Z= 0.278 Chirality : 0.040 0.131 1679 Planarity : 0.004 0.036 1936 Dihedral : 5.277 45.034 1463 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.94 % Allowed : 12.60 % Favored : 85.46 % 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: -0.61 (0.23), residues: 1296 helix: 0.12 (0.17), residues: 993 sheet: None (None), residues: 0 loop : -1.87 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 131 HIS 0.003 0.001 HIS G 118 PHE 0.012 0.001 PHE D 114 TYR 0.012 0.001 TYR I 137 ARG 0.004 0.000 ARG A 182 *********************** 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 230 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 LEU cc_start: 0.4080 (OUTLIER) cc_final: 0.3857 (tt) REVERT: E 113 HIS cc_start: 0.7010 (t-170) cc_final: 0.6604 (t-170) REVERT: H 112 LEU cc_start: 0.4086 (OUTLIER) cc_final: 0.3829 (mm) REVERT: I 139 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7560 (mttt) REVERT: L 167 PRO cc_start: 0.8299 (Cg_exo) cc_final: 0.8081 (Cg_endo) REVERT: M 190 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6487 (mp0) REVERT: O 146 TYR cc_start: 0.7258 (t80) cc_final: 0.7012 (t80) outliers start: 23 outliers final: 15 residues processed: 224 average time/residue: 0.2207 time to fit residues: 71.0515 Evaluate side-chains 202 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 187 TYR 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 172 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 166 THR 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 154 THR Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain P residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 185 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.163914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.149835 restraints weight = 13712.155| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.10 r_work: 0.3530 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.9405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11247 Z= 0.207 Angle : 0.660 12.450 15262 Z= 0.334 Chirality : 0.043 0.256 1679 Planarity : 0.004 0.036 1936 Dihedral : 5.397 45.866 1463 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.54 % Allowed : 13.19 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1296 helix: 0.31 (0.17), residues: 997 sheet: None (None), residues: 0 loop : -1.77 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 131 HIS 0.006 0.001 HIS G 118 PHE 0.015 0.002 PHE A 114 TYR 0.017 0.001 TYR A 146 ARG 0.006 0.001 ARG F 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 1.346 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: A 134 ASP cc_start: 0.8025 (m-30) cc_final: 0.7812 (m-30) REVERT: B 159 MET cc_start: 0.6635 (tpt) cc_final: 0.6242 (mmm) REVERT: C 133 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8135 (mp) REVERT: D 159 MET cc_start: 0.8832 (mmm) cc_final: 0.8409 (mmm) REVERT: E 113 HIS cc_start: 0.7414 (t-170) cc_final: 0.7109 (t-170) REVERT: G 134 ASP cc_start: 0.8038 (m-30) cc_final: 0.7679 (m-30) REVERT: I 112 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6899 (mm) REVERT: I 137 TYR cc_start: 0.8723 (t80) cc_final: 0.8474 (t80) REVERT: I 187 TYR cc_start: 0.8013 (p90) cc_final: 0.7381 (p90) REVERT: I 190 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7656 (tt0) REVERT: I 194 ARG cc_start: 0.6073 (ttp80) cc_final: 0.5839 (tmt-80) REVERT: J 112 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5817 (tm) REVERT: K 116 ASP cc_start: 0.8472 (m-30) cc_final: 0.8096 (m-30) REVERT: K 161 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8507 (tppt) REVERT: K 193 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7289 (mt-10) REVERT: L 116 ASP cc_start: 0.8078 (t70) cc_final: 0.7840 (m-30) REVERT: M 117 GLN cc_start: 0.7685 (tt0) cc_final: 0.7264 (tt0) REVERT: M 158 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8628 (mttp) REVERT: M 175 ASP cc_start: 0.8195 (p0) cc_final: 0.7643 (m-30) outliers start: 30 outliers final: 17 residues processed: 286 average time/residue: 0.2501 time to fit residues: 98.7558 Evaluate side-chains 237 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 172 THR 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 142 THR Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 158 LYS 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: 0.9990 chunk 35 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN D 117 GLN F 128 ASN G 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.157866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.144476 restraints weight = 13913.915| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.09 r_work: 0.3469 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 1.0399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11247 Z= 0.167 Angle : 0.587 10.897 15262 Z= 0.297 Chirality : 0.041 0.146 1679 Planarity : 0.004 0.038 1936 Dihedral : 5.193 46.429 1463 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.45 % Allowed : 14.79 % Favored : 82.76 % 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: 0.13 (0.23), residues: 1296 helix: 0.79 (0.18), residues: 892 sheet: None (None), residues: 0 loop : -1.43 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 131 HIS 0.003 0.001 HIS E 118 PHE 0.017 0.001 PHE A 114 TYR 0.018 0.001 TYR H 146 ARG 0.005 0.000 ARG K 194 *********************** 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 278 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 1.301 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: symmetry clash REVERT: B 159 MET cc_start: 0.7487 (tpt) cc_final: 0.7140 (mmm) REVERT: B 183 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6352 (mm-30) REVERT: D 159 MET cc_start: 0.8941 (mmm) cc_final: 0.8509 (mmm) REVERT: F 128 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8163 (p0) REVERT: G 134 ASP cc_start: 0.8375 (m-30) cc_final: 0.8015 (m-30) REVERT: I 112 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6517 (mm) REVERT: I 137 TYR cc_start: 0.8710 (t80) cc_final: 0.8255 (t80) REVERT: I 176 LEU cc_start: 0.8679 (tt) cc_final: 0.8225 (mp) REVERT: I 188 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8437 (tp) REVERT: I 190 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7604 (tt0) REVERT: I 194 ARG cc_start: 0.6050 (ttp80) cc_final: 0.5697 (tmt-80) REVERT: J 112 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5879 (tm) REVERT: J 139 LYS cc_start: 0.8660 (mttt) cc_final: 0.8411 (mttt) REVERT: M 112 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7032 (tm) REVERT: M 158 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8730 (mttp) REVERT: M 175 ASP cc_start: 0.8196 (p0) cc_final: 0.7694 (m-30) REVERT: M 190 GLU cc_start: 0.7950 (mp0) cc_final: 0.7507 (mp0) REVERT: N 159 MET cc_start: 0.1221 (ppp) cc_final: 0.0433 (tpp) outliers start: 29 outliers final: 14 residues processed: 267 average time/residue: 0.2311 time to fit residues: 86.5152 Evaluate side-chains 247 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 172 THR 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 115 ILE Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 158 LYS Chi-restraints excluded: chain N residue 154 THR 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: 1.9990 chunk 7 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN D 147 GLN M 145 GLN O 117 GLN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.143702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.130603 restraints weight = 14121.160| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.17 r_work: 0.3300 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 1.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 11247 Z= 0.240 Angle : 0.664 10.967 15262 Z= 0.334 Chirality : 0.044 0.235 1679 Planarity : 0.004 0.039 1936 Dihedral : 5.440 46.338 1463 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.70 % Allowed : 15.55 % Favored : 81.74 % 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: 0.21 (0.24), residues: 1296 helix: 0.68 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 131 HIS 0.008 0.001 HIS G 113 PHE 0.017 0.001 PHE A 114 TYR 0.019 0.002 TYR L 146 ARG 0.007 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 1.229 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 164 SER cc_start: 0.7992 (t) cc_final: 0.7625 (p) REVERT: B 190 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7335 (mt-10) REVERT: D 112 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5322 (mt) REVERT: D 159 MET cc_start: 0.9113 (mmm) cc_final: 0.8905 (mmm) REVERT: E 165 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8847 (m-80) REVERT: F 129 VAL cc_start: 0.8931 (t) cc_final: 0.8722 (t) REVERT: G 134 ASP cc_start: 0.8500 (m-30) cc_final: 0.8152 (m-30) REVERT: I 188 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8568 (tp) REVERT: I 194 ARG cc_start: 0.6359 (ttp80) cc_final: 0.6011 (tmt-80) REVERT: J 134 ASP cc_start: 0.8829 (m-30) cc_final: 0.8622 (m-30) REVERT: J 139 LYS cc_start: 0.8756 (mttt) cc_final: 0.8532 (mttt) REVERT: K 116 ASP cc_start: 0.8592 (m-30) cc_final: 0.8304 (m-30) REVERT: L 183 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7182 (mm-30) REVERT: L 193 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8246 (mt-10) REVERT: M 112 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7221 (tm) REVERT: M 155 ASN cc_start: 0.8789 (t0) cc_final: 0.8547 (m-40) REVERT: M 158 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9047 (mttp) REVERT: M 174 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8298 (mtpp) REVERT: M 175 ASP cc_start: 0.8298 (p0) cc_final: 0.7944 (m-30) REVERT: N 163 PHE cc_start: 0.8642 (m-80) cc_final: 0.8242 (m-80) REVERT: O 161 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8633 (tptt) outliers start: 32 outliers final: 20 residues processed: 281 average time/residue: 0.2990 time to fit residues: 112.9317 Evaluate side-chains 265 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 178 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 F residue 154 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 154 THR 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 115 ILE Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 158 LYS Chi-restraints excluded: chain N residue 154 THR 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: 0.9990 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 HIS J 118 HIS O 117 GLN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.140304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128076 restraints weight = 14155.455| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.13 r_work: 0.3265 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 1.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 11247 Z= 0.200 Angle : 0.619 8.963 15262 Z= 0.311 Chirality : 0.042 0.189 1679 Planarity : 0.004 0.039 1936 Dihedral : 5.296 47.262 1463 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.11 % Allowed : 16.40 % 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: 0.03 (0.24), residues: 1296 helix: 0.62 (0.17), residues: 1042 sheet: None (None), residues: 0 loop : -2.25 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 131 HIS 0.004 0.001 HIS P 113 PHE 0.015 0.001 PHE A 114 TYR 0.018 0.001 TYR I 137 ARG 0.006 0.001 ARG O 150 *********************** 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 272 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 1.237 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: E 147 GLN cc_start: 0.9006 (pt0) cc_final: 0.8751 (pt0) REVERT: E 165 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: E 182 ARG cc_start: 0.8505 (mtt90) cc_final: 0.8292 (mtt-85) REVERT: G 134 ASP cc_start: 0.8442 (m-30) cc_final: 0.8040 (m-30) REVERT: I 188 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8557 (tp) REVERT: I 194 ARG cc_start: 0.6458 (ttp80) cc_final: 0.6081 (tmt-80) REVERT: J 112 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6218 (tm) REVERT: K 116 ASP cc_start: 0.8483 (m-30) cc_final: 0.8204 (m-30) REVERT: K 129 VAL cc_start: 0.8961 (t) cc_final: 0.8742 (t) REVERT: K 184 SER cc_start: 0.8753 (t) cc_final: 0.8476 (t) REVERT: L 182 ARG cc_start: 0.8473 (mtt90) cc_final: 0.7938 (mtm-85) REVERT: L 183 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7201 (mm-30) REVERT: M 112 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7106 (tm) REVERT: M 158 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8952 (mttp) REVERT: M 174 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8291 (mtpp) REVERT: M 175 ASP cc_start: 0.8206 (p0) cc_final: 0.7875 (m-30) outliers start: 25 outliers final: 12 residues processed: 263 average time/residue: 0.2727 time to fit residues: 96.4697 Evaluate side-chains 249 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G 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 115 ILE Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 158 LYS Chi-restraints excluded: chain O residue 112 LEU 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: 0.0070 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 0.0030 chunk 56 optimal weight: 0.0980 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 GLN O 117 GLN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.143440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.131251 restraints weight = 14071.776| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.10 r_work: 0.3311 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 1.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11247 Z= 0.165 Angle : 0.598 8.681 15262 Z= 0.300 Chirality : 0.041 0.162 1679 Planarity : 0.004 0.039 1936 Dihedral : 5.038 47.798 1460 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.03 % Allowed : 16.48 % 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: 0.18 (0.24), residues: 1296 helix: 0.73 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -2.22 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 131 HIS 0.005 0.001 HIS E 113 PHE 0.015 0.001 PHE A 114 TYR 0.020 0.001 TYR L 146 ARG 0.007 0.001 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 1.281 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: E 147 GLN cc_start: 0.9062 (pt0) cc_final: 0.8809 (pt0) REVERT: E 165 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: E 182 ARG cc_start: 0.8521 (mtt90) cc_final: 0.8221 (mtt-85) REVERT: F 183 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7467 (mm-30) REVERT: G 134 ASP cc_start: 0.8436 (m-30) cc_final: 0.7962 (m-30) REVERT: H 134 ASP cc_start: 0.8069 (m-30) cc_final: 0.7780 (m-30) REVERT: I 188 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8383 (tp) REVERT: I 194 ARG cc_start: 0.6484 (ttp80) cc_final: 0.6080 (tmt-80) REVERT: J 112 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6364 (tm) REVERT: K 116 ASP cc_start: 0.8400 (m-30) cc_final: 0.8086 (m-30) REVERT: K 184 SER cc_start: 0.8712 (t) cc_final: 0.8428 (t) REVERT: L 182 ARG cc_start: 0.8476 (mtt90) cc_final: 0.7963 (mtm-85) REVERT: L 183 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7267 (mm-30) REVERT: M 112 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7068 (tm) REVERT: M 174 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8290 (mtpp) outliers start: 24 outliers final: 16 residues processed: 248 average time/residue: 0.2502 time to fit residues: 85.5577 Evaluate side-chains 240 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G 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 115 ILE Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 188 LEU 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 140 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 112 LEU 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: 0.4980 chunk 72 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.126054 restraints weight = 14068.847| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.05 r_work: 0.3242 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 1.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11247 Z= 0.199 Angle : 0.633 12.067 15262 Z= 0.312 Chirality : 0.042 0.181 1679 Planarity : 0.004 0.039 1936 Dihedral : 5.063 47.353 1460 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.52 % Allowed : 16.99 % 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: 0.21 (0.24), residues: 1296 helix: 0.74 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -2.17 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 169 HIS 0.004 0.001 HIS E 113 PHE 0.014 0.001 PHE A 114 TYR 0.019 0.001 TYR L 146 ARG 0.008 0.001 ARG C 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 1.299 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: 0.7783 (mm-30) cc_final: 0.7518 (tp30) REVERT: E 147 GLN cc_start: 0.9138 (pt0) cc_final: 0.8919 (pt0) REVERT: E 165 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: E 182 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8180 (mtt-85) REVERT: F 183 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7570 (mm-30) REVERT: G 134 ASP cc_start: 0.8423 (m-30) cc_final: 0.7979 (m-30) REVERT: H 134 ASP cc_start: 0.8071 (m-30) cc_final: 0.7699 (m-30) REVERT: I 141 LEU cc_start: 0.8525 (mp) cc_final: 0.8318 (mt) REVERT: I 188 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8339 (tp) REVERT: I 194 ARG cc_start: 0.6498 (ttp80) cc_final: 0.6077 (tmt-80) REVERT: J 112 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6468 (tm) REVERT: J 194 ARG cc_start: 0.6202 (mmm-85) cc_final: 0.5953 (mtp180) REVERT: K 184 SER cc_start: 0.8885 (t) cc_final: 0.8628 (t) REVERT: L 182 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7976 (mtm-85) REVERT: L 183 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7259 (mm-30) REVERT: M 155 ASN cc_start: 0.8999 (m-40) cc_final: 0.8590 (m-40) REVERT: M 176 LEU cc_start: 0.8615 (tt) cc_final: 0.8195 (mt) REVERT: N 159 MET cc_start: 0.8546 (mmm) cc_final: 0.8308 (tpt) REVERT: O 184 SER cc_start: 0.8426 (t) cc_final: 0.8141 (t) outliers start: 18 outliers final: 9 residues processed: 243 average time/residue: 0.2492 time to fit residues: 83.1976 Evaluate side-chains 238 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain O residue 112 LEU 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: 1.9990 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN L 185 GLN O 117 GLN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.136009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.124951 restraints weight = 14085.503| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.04 r_work: 0.3228 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 1.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11247 Z= 0.191 Angle : 0.626 12.325 15262 Z= 0.308 Chirality : 0.042 0.191 1679 Planarity : 0.004 0.039 1936 Dihedral : 4.933 47.288 1458 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 17.84 % Favored : 80.73 % 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: 0.26 (0.24), residues: 1296 helix: 0.78 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -2.14 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 131 HIS 0.005 0.001 HIS E 113 PHE 0.014 0.001 PHE A 114 TYR 0.018 0.001 TYR L 146 ARG 0.007 0.001 ARG O 150 =============================================================================== Job complete usr+sys time: 4998.42 seconds wall clock time: 89 minutes 31.79 seconds (5371.79 seconds total)