Starting phenix.real_space_refine on Wed Sep 17 18:56:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1h_8902/09_2025/6n1h_8902.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1h_8902/09_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_8902/09_2025/6n1h_8902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1h_8902/09_2025/6n1h_8902.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1h_8902/09_2025/6n1h_8902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1h_8902/09_2025/6n1h_8902.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.82, per 1000 atoms: 0.26 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: 1.06 Conformation dependent library (CDL) restraints added in 396.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2622 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 0 sheets defined 88.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 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: 1.61 Time building geometry restraints manager: 1.38 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.432 11249 Z= 0.562 Angle : 1.129 10.738 15262 Z= 0.652 Chirality : 0.058 0.271 1679 Planarity : 0.008 0.062 1936 Dihedral : 12.227 71.692 4143 Min Nonbonded Distance : 0.657 Molprobity Statistics. All-atom Clashscore : 31.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.002 ARG A 125 TYR 0.006 0.002 TYR K 146 PHE 0.021 0.004 PHE K 163 TRP 0.026 0.004 TRP N 131 HIS 0.003 0.001 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00616 (11247) covalent geometry : angle 1.12862 (15262) hydrogen bonds : bond 0.28419 ( 528) hydrogen bonds : angle 9.46194 ( 1488) Misc. bond : bond 0.36714 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 0.438 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: 0.6139 (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: 0.1116 time to fit residues: 41.7896 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 : 0.416 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 HIS D 147 GLN E 118 HIS ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 HIS I 113 HIS J 118 HIS J 185 GLN K 118 HIS L 145 GLN N 185 GLN O 117 GLN O 118 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.172184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.156405 restraints weight = 13984.527| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.23 r_work: 0.3602 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11249 Z= 0.215 Angle : 0.754 9.821 15262 Z= 0.393 Chirality : 0.046 0.208 1679 Planarity : 0.007 0.066 1936 Dihedral : 6.833 49.710 1500 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.28 % Allowed : 7.19 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.36 (0.17), residues: 1296 helix: -2.48 (0.12), residues: 1023 sheet: None (None), residues: 0 loop : -3.60 (0.26), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 160 TYR 0.022 0.003 TYR B 187 PHE 0.023 0.002 PHE H 114 TRP 0.022 0.002 TRP C 171 HIS 0.006 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00450 (11247) covalent geometry : angle 0.75368 (15262) hydrogen bonds : bond 0.03012 ( 528) hydrogen bonds : angle 5.17618 ( 1488) Misc. bond : bond 0.00449 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 THR cc_start: 0.7900 (p) cc_final: 0.7590 (p) REVERT: D 170 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7549 (p0) REVERT: E 113 HIS cc_start: 0.7054 (t-170) cc_final: 0.6789 (t-170) REVERT: E 115 ILE cc_start: 0.8119 (mm) cc_final: 0.7856 (mm) REVERT: E 116 ASP cc_start: 0.7365 (m-30) cc_final: 0.7159 (m-30) REVERT: H 112 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5604 (tm) REVERT: I 139 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7386 (mtmt) REVERT: J 123 ILE cc_start: 0.7880 (mm) cc_final: 0.7565 (mm) REVERT: K 144 GLU cc_start: 0.6880 (tp30) cc_final: 0.6434 (tt0) outliers start: 27 outliers final: 15 residues processed: 257 average time/residue: 0.1233 time to fit residues: 43.5957 Evaluate side-chains 203 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 166 THR Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain 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 166 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.0070 chunk 124 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 113 HIS B 128 ASN ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN L 155 ASN O 117 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.165511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.150157 restraints weight = 13903.745| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.22 r_work: 0.3533 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.7691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11249 Z= 0.142 Angle : 0.644 9.242 15262 Z= 0.327 Chirality : 0.041 0.137 1679 Planarity : 0.005 0.042 1936 Dihedral : 5.591 54.086 1469 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.45 % Allowed : 11.16 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.22), residues: 1296 helix: -0.71 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.24 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 182 TYR 0.022 0.001 TYR H 187 PHE 0.022 0.001 PHE D 114 TRP 0.023 0.001 TRP B 171 HIS 0.010 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00314 (11247) covalent geometry : angle 0.64391 (15262) hydrogen bonds : bond 0.04015 ( 528) hydrogen bonds : angle 4.67598 ( 1488) Misc. bond : bond 0.00379 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8098 (t0) cc_final: 0.7812 (t70) REVERT: E 113 HIS cc_start: 0.7527 (t-170) cc_final: 0.7087 (t-170) REVERT: F 159 MET cc_start: 0.8558 (tpt) cc_final: 0.8117 (mmp) REVERT: G 134 ASP cc_start: 0.7302 (m-30) cc_final: 0.7006 (m-30) REVERT: I 139 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (mttt) REVERT: I 187 TYR cc_start: 0.7449 (p90) cc_final: 0.7116 (p90) REVERT: J 112 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5620 (tm) REVERT: J 164 SER cc_start: 0.9210 (t) cc_final: 0.9003 (t) REVERT: K 134 ASP cc_start: 0.8475 (m-30) cc_final: 0.8216 (m-30) REVERT: K 136 LEU cc_start: 0.8683 (mt) cc_final: 0.8381 (mt) REVERT: M 117 GLN cc_start: 0.7208 (tt0) cc_final: 0.6930 (tt0) REVERT: M 190 GLU cc_start: 0.7455 (mp0) cc_final: 0.7188 (mp0) REVERT: N 116 ASP cc_start: 0.6979 (m-30) cc_final: 0.6771 (m-30) REVERT: N 159 MET cc_start: 0.2202 (ppp) cc_final: 0.0837 (tpp) REVERT: O 116 ASP cc_start: 0.8609 (m-30) cc_final: 0.8402 (m-30) outliers start: 29 outliers final: 16 residues processed: 259 average time/residue: 0.1197 time to fit residues: 42.9845 Evaluate side-chains 217 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L 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 11 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN C 128 ASN C 185 GLN ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 ASN O 117 GLN P 113 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.140033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.127555 restraints weight = 14222.406| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.12 r_work: 0.3264 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 1.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11249 Z= 0.213 Angle : 0.781 12.197 15262 Z= 0.389 Chirality : 0.047 0.187 1679 Planarity : 0.005 0.041 1936 Dihedral : 6.165 52.742 1464 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.87 % Allowed : 12.34 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.22), residues: 1296 helix: -0.18 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.49 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 160 TYR 0.013 0.002 TYR H 187 PHE 0.015 0.002 PHE K 114 TRP 0.019 0.002 TRP J 131 HIS 0.010 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00509 (11247) covalent geometry : angle 0.78053 (15262) hydrogen bonds : bond 0.03911 ( 528) hydrogen bonds : angle 5.17836 ( 1488) Misc. bond : bond 0.00545 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 319 time to evaluate : 0.462 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: B 128 ASN cc_start: 0.7957 (t0) cc_final: 0.7673 (t0) REVERT: D 112 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7042 (tm) REVERT: D 134 ASP cc_start: 0.8643 (m-30) cc_final: 0.8272 (m-30) REVERT: E 117 GLN cc_start: 0.8769 (tt0) cc_final: 0.8537 (tt0) REVERT: F 116 ASP cc_start: 0.8162 (m-30) cc_final: 0.7956 (m-30) REVERT: F 155 ASN cc_start: 0.8613 (t0) cc_final: 0.8412 (m-40) REVERT: F 184 SER cc_start: 0.8898 (t) cc_final: 0.8070 (t) REVERT: G 134 ASP cc_start: 0.8421 (m-30) cc_final: 0.7935 (m-30) REVERT: G 147 GLN cc_start: 0.8851 (mt0) cc_final: 0.8605 (mt0) REVERT: H 134 ASP cc_start: 0.8094 (m-30) cc_final: 0.7861 (m-30) REVERT: I 142 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8843 (m) REVERT: I 147 GLN cc_start: 0.8610 (mt0) cc_final: 0.8361 (mt0) REVERT: I 194 ARG cc_start: 0.6641 (ttp80) cc_final: 0.6268 (tmt-80) REVERT: J 112 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6648 (tm) REVERT: J 144 GLU cc_start: 0.7996 (mp0) cc_final: 0.7766 (mt-10) REVERT: K 146 TYR cc_start: 0.9321 (t80) cc_final: 0.8892 (t80) REVERT: K 164 SER cc_start: 0.9019 (t) cc_final: 0.8580 (m) REVERT: K 191 ASP cc_start: 0.8347 (t70) cc_final: 0.8025 (t0) REVERT: L 142 THR cc_start: 0.9079 (p) cc_final: 0.8879 (p) REVERT: L 147 GLN cc_start: 0.8775 (mt0) cc_final: 0.8118 (mt0) REVERT: L 193 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7993 (mt-10) REVERT: M 143 ASP cc_start: 0.8551 (t0) cc_final: 0.7960 (t0) REVERT: M 147 GLN cc_start: 0.8563 (mt0) cc_final: 0.8341 (mt0) REVERT: M 174 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8314 (mtmt) REVERT: M 175 ASP cc_start: 0.8312 (p0) cc_final: 0.7675 (p0) REVERT: N 159 MET cc_start: 0.3052 (ppp) cc_final: 0.2665 (tpp) REVERT: O 143 ASP cc_start: 0.8511 (t70) cc_final: 0.7380 (t70) outliers start: 34 outliers final: 17 residues processed: 339 average time/residue: 0.1360 time to fit residues: 62.0235 Evaluate side-chains 293 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 272 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 154 THR 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 F residue 112 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain O residue 115 ILE 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 124 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 93 optimal weight: 0.0010 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 94 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 overall best weight: 0.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS B 113 HIS B 145 GLN D 147 GLN F 145 GLN G 117 GLN G 128 ASN G 185 GLN ** L 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 HIS N 118 HIS O 117 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.145162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132726 restraints weight = 14120.173| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.14 r_work: 0.3343 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 1.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11249 Z= 0.104 Angle : 0.594 9.498 15262 Z= 0.295 Chirality : 0.041 0.157 1679 Planarity : 0.004 0.040 1936 Dihedral : 5.387 48.028 1464 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.20 % Allowed : 13.44 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.23), residues: 1296 helix: 0.13 (0.17), residues: 966 sheet: None (None), residues: 0 loop : -1.43 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 182 TYR 0.013 0.001 TYR D 137 PHE 0.014 0.001 PHE D 114 TRP 0.015 0.001 TRP G 171 HIS 0.004 0.001 HIS N 118 Details of bonding type rmsd covalent geometry : bond 0.00229 (11247) covalent geometry : angle 0.59402 (15262) hydrogen bonds : bond 0.02612 ( 528) hydrogen bonds : angle 4.28588 ( 1488) Misc. bond : bond 0.00328 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 278 time to evaluate : 0.423 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. REVERT: B 128 ASN cc_start: 0.8024 (t0) cc_final: 0.7615 (t0) REVERT: B 183 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7054 (mm-30) REVERT: B 190 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7127 (mt-10) REVERT: D 139 LYS cc_start: 0.8151 (mppt) cc_final: 0.7833 (mmtm) REVERT: D 159 MET cc_start: 0.9157 (mmm) cc_final: 0.8923 (mmm) REVERT: D 190 GLU cc_start: 0.7880 (mp0) cc_final: 0.7637 (mp0) REVERT: F 116 ASP cc_start: 0.8144 (m-30) cc_final: 0.7916 (m-30) REVERT: H 134 ASP cc_start: 0.8145 (m-30) cc_final: 0.7860 (m-30) REVERT: I 137 TYR cc_start: 0.8627 (t80) cc_final: 0.8248 (t80) REVERT: I 194 ARG cc_start: 0.6611 (ttp80) cc_final: 0.6212 (tmt-80) REVERT: J 112 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5786 (mm) REVERT: J 144 GLU cc_start: 0.8047 (mp0) cc_final: 0.7813 (mp0) REVERT: K 146 TYR cc_start: 0.9402 (t80) cc_final: 0.8843 (t80) REVERT: L 183 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7209 (mm-30) REVERT: L 193 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8200 (mt-10) REVERT: M 112 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6457 (tm) REVERT: M 143 ASP cc_start: 0.8367 (t0) cc_final: 0.7641 (t70) REVERT: M 147 GLN cc_start: 0.8307 (mt0) cc_final: 0.8052 (mt0) REVERT: M 175 ASP cc_start: 0.8303 (p0) cc_final: 0.8043 (m-30) REVERT: M 193 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8229 (mt-10) outliers start: 26 outliers final: 9 residues processed: 292 average time/residue: 0.1288 time to fit residues: 51.0343 Evaluate side-chains 262 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 251 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain O residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 GLN F 145 GLN G 117 GLN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 GLN O 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.131392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.121346 restraints weight = 14154.972| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 0.94 r_work: 0.3157 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 1.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 11249 Z= 0.179 Angle : 0.719 13.574 15262 Z= 0.346 Chirality : 0.045 0.247 1679 Planarity : 0.005 0.039 1936 Dihedral : 5.411 48.610 1460 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.54 % Allowed : 13.95 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.23), residues: 1296 helix: 0.23 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -2.51 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 194 TYR 0.019 0.002 TYR C 137 PHE 0.017 0.002 PHE K 114 TRP 0.014 0.002 TRP A 169 HIS 0.007 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00449 (11247) covalent geometry : angle 0.71879 (15262) hydrogen bonds : bond 0.03572 ( 528) hydrogen bonds : angle 4.59856 ( 1488) Misc. bond : bond 0.00719 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.443 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. REVERT: B 183 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 112 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6851 (tp) REVERT: D 139 LYS cc_start: 0.8412 (mppt) cc_final: 0.7939 (mmtm) REVERT: D 144 GLU cc_start: 0.8172 (tt0) cc_final: 0.7715 (tt0) REVERT: D 190 GLU cc_start: 0.7925 (mp0) cc_final: 0.7559 (mm-30) REVERT: E 145 GLN cc_start: 0.9276 (mt0) cc_final: 0.9043 (mt0) REVERT: G 147 GLN cc_start: 0.8658 (mt0) cc_final: 0.8255 (mt0) REVERT: H 134 ASP cc_start: 0.8155 (m-30) cc_final: 0.7895 (m-30) REVERT: I 194 ARG cc_start: 0.6681 (ttp80) cc_final: 0.6218 (tmt-80) REVERT: J 112 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6650 (tm) REVERT: J 139 LYS cc_start: 0.8898 (mttt) cc_final: 0.8635 (mttt) REVERT: J 144 GLU cc_start: 0.7925 (mp0) cc_final: 0.7603 (mp0) REVERT: K 144 GLU cc_start: 0.7916 (tt0) cc_final: 0.7605 (tt0) REVERT: K 164 SER cc_start: 0.8879 (t) cc_final: 0.8562 (m) REVERT: L 183 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7314 (mm-30) REVERT: L 193 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8314 (mt-10) REVERT: M 115 ILE cc_start: 0.8317 (mm) cc_final: 0.8004 (mm) REVERT: M 155 ASN cc_start: 0.8955 (m-40) cc_final: 0.8736 (m-40) REVERT: M 187 TYR cc_start: 0.8015 (p90) cc_final: 0.7704 (p90) outliers start: 30 outliers final: 15 residues processed: 277 average time/residue: 0.1206 time to fit residues: 46.1807 Evaluate side-chains 264 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain H residue 112 LEU 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 117 GLN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS D 147 GLN G 128 ASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN M 179 GLN O 117 GLN O 179 GLN P 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.132618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.120834 restraints weight = 14165.249| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.18 r_work: 0.3208 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 1.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11249 Z= 0.114 Angle : 0.629 11.645 15262 Z= 0.304 Chirality : 0.043 0.200 1679 Planarity : 0.004 0.039 1936 Dihedral : 4.968 47.616 1458 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.61 % Allowed : 15.38 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.23), residues: 1296 helix: 0.78 (0.17), residues: 951 sheet: None (None), residues: 0 loop : -1.58 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 194 TYR 0.020 0.001 TYR K 146 PHE 0.013 0.001 PHE D 114 TRP 0.025 0.001 TRP N 131 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00275 (11247) covalent geometry : angle 0.62926 (15262) hydrogen bonds : bond 0.02837 ( 528) hydrogen bonds : angle 4.25021 ( 1488) Misc. bond : bond 0.00508 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.445 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 133 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8909 (mt) REVERT: D 112 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6408 (tp) REVERT: D 139 LYS cc_start: 0.8269 (mppt) cc_final: 0.7932 (mmtm) REVERT: D 144 GLU cc_start: 0.8154 (tt0) cc_final: 0.7767 (tt0) REVERT: D 191 ASP cc_start: 0.9003 (t0) cc_final: 0.8736 (t0) REVERT: E 145 GLN cc_start: 0.9257 (mt0) cc_final: 0.9034 (mt0) REVERT: G 134 ASP cc_start: 0.8497 (m-30) cc_final: 0.8113 (m-30) REVERT: G 182 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8212 (mtm-85) REVERT: H 134 ASP cc_start: 0.8232 (m-30) cc_final: 0.7973 (m-30) REVERT: I 194 ARG cc_start: 0.6813 (ttp80) cc_final: 0.6425 (tmt-80) REVERT: J 112 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6353 (tm) REVERT: J 144 GLU cc_start: 0.7881 (mp0) cc_final: 0.7650 (mp0) REVERT: K 146 TYR cc_start: 0.9458 (t80) cc_final: 0.9008 (t80) REVERT: L 193 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8330 (mt-10) REVERT: M 175 ASP cc_start: 0.8284 (p0) cc_final: 0.8007 (m-30) REVERT: N 158 LYS cc_start: 0.7949 (mttp) cc_final: 0.7596 (mttp) REVERT: O 152 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5444 (mt-10) outliers start: 19 outliers final: 9 residues processed: 266 average time/residue: 0.1311 time to fit residues: 46.9953 Evaluate side-chains 253 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain H residue 112 LEU 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 177 LEU Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 152 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 GLN G 128 ASN H 145 GLN N 128 ASN O 117 GLN O 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.129145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.117544 restraints weight = 14306.101| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.22 r_work: 0.3183 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 1.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11249 Z= 0.127 Angle : 0.641 10.510 15262 Z= 0.310 Chirality : 0.043 0.176 1679 Planarity : 0.004 0.037 1936 Dihedral : 4.941 48.321 1458 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.94 % Allowed : 15.72 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.23), residues: 1296 helix: 0.74 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -2.31 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 194 TYR 0.020 0.001 TYR I 137 PHE 0.014 0.001 PHE D 114 TRP 0.028 0.001 TRP N 131 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00309 (11247) covalent geometry : angle 0.64097 (15262) hydrogen bonds : bond 0.02996 ( 528) hydrogen bonds : angle 4.26035 ( 1488) Misc. bond : bond 0.00552 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.436 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 133 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8971 (mt) REVERT: D 112 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6319 (tp) REVERT: D 139 LYS cc_start: 0.8286 (mppt) cc_final: 0.7916 (mmtm) REVERT: D 144 GLU cc_start: 0.8119 (tt0) cc_final: 0.7623 (tt0) REVERT: D 190 GLU cc_start: 0.7543 (mp0) cc_final: 0.7134 (mm-30) REVERT: E 145 GLN cc_start: 0.9268 (mt0) cc_final: 0.9039 (mt0) REVERT: G 130 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8171 (mm-30) REVERT: G 134 ASP cc_start: 0.8511 (m-30) cc_final: 0.8098 (m-30) REVERT: G 147 GLN cc_start: 0.8784 (mt0) cc_final: 0.8527 (mt0) REVERT: G 154 THR cc_start: 0.8908 (m) cc_final: 0.8673 (m) REVERT: G 182 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.8283 (mtm-85) REVERT: G 194 ARG cc_start: 0.7224 (ttp80) cc_final: 0.6767 (ttp80) REVERT: H 134 ASP cc_start: 0.8256 (m-30) cc_final: 0.7999 (m-30) REVERT: H 182 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.7810 (mtt-85) REVERT: I 194 ARG cc_start: 0.7068 (ttp80) cc_final: 0.6521 (tmt-80) REVERT: J 112 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6445 (tm) REVERT: K 117 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: K 164 SER cc_start: 0.8917 (t) cc_final: 0.8586 (m) REVERT: L 182 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: L 193 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8302 (mt-10) REVERT: M 175 ASP cc_start: 0.8156 (p0) cc_final: 0.7728 (p0) REVERT: N 128 ASN cc_start: 0.8312 (t0) cc_final: 0.7783 (t0) REVERT: N 158 LYS cc_start: 0.8276 (mttp) cc_final: 0.7957 (mttp) REVERT: O 152 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.5404 (mt-10) outliers start: 23 outliers final: 12 residues processed: 257 average time/residue: 0.1312 time to fit residues: 45.5313 Evaluate side-chains 255 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain H residue 112 LEU 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 117 GLN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 152 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 GLN G 128 ASN O 117 GLN O 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.116064 restraints weight = 14205.019| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.20 r_work: 0.3125 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 1.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11249 Z= 0.134 Angle : 0.659 14.333 15262 Z= 0.315 Chirality : 0.044 0.217 1679 Planarity : 0.004 0.037 1936 Dihedral : 4.963 47.459 1458 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.86 % Allowed : 16.15 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.23), residues: 1296 helix: 0.82 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -2.32 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 194 TYR 0.019 0.001 TYR I 137 PHE 0.013 0.001 PHE D 114 TRP 0.024 0.001 TRP N 131 HIS 0.008 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00330 (11247) covalent geometry : angle 0.65859 (15262) hydrogen bonds : bond 0.02988 ( 528) hydrogen bonds : angle 4.27062 ( 1488) Misc. bond : bond 0.00552 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.456 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 133 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8995 (mt) REVERT: D 112 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6292 (tp) REVERT: D 139 LYS cc_start: 0.8351 (mppt) cc_final: 0.8003 (mmtm) REVERT: D 144 GLU cc_start: 0.8151 (tt0) cc_final: 0.7650 (tt0) REVERT: E 145 GLN cc_start: 0.9278 (mt0) cc_final: 0.9042 (mt0) REVERT: G 130 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8179 (mm-30) REVERT: G 134 ASP cc_start: 0.8521 (m-30) cc_final: 0.8106 (m-30) REVERT: G 147 GLN cc_start: 0.8760 (mt0) cc_final: 0.8507 (mt0) REVERT: G 194 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6661 (ttp80) REVERT: H 134 ASP cc_start: 0.8252 (m-30) cc_final: 0.8000 (m-30) REVERT: I 194 ARG cc_start: 0.7096 (ttp80) cc_final: 0.6541 (tmt-80) REVERT: J 112 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6460 (tm) REVERT: K 117 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: K 164 SER cc_start: 0.8904 (t) cc_final: 0.8598 (m) REVERT: L 182 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8259 (mtm-85) REVERT: L 193 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8323 (mt-10) REVERT: M 175 ASP cc_start: 0.8175 (p0) cc_final: 0.7813 (m-30) REVERT: N 122 LEU cc_start: 0.6377 (tt) cc_final: 0.6043 (tp) REVERT: N 144 GLU cc_start: 0.8321 (tt0) cc_final: 0.8118 (tt0) REVERT: N 158 LYS cc_start: 0.8353 (mttp) cc_final: 0.8001 (mttp) REVERT: O 152 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5452 (mt-10) outliers start: 22 outliers final: 12 residues processed: 258 average time/residue: 0.1319 time to fit residues: 45.9672 Evaluate side-chains 255 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain H residue 112 LEU 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 117 GLN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 152 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 HIS E 113 HIS O 117 GLN O 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.115887 restraints weight = 14319.553| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.20 r_work: 0.3167 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 1.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11249 Z= 0.125 Angle : 0.643 12.812 15262 Z= 0.310 Chirality : 0.043 0.209 1679 Planarity : 0.004 0.037 1936 Dihedral : 4.906 47.808 1458 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.44 % Allowed : 16.40 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1296 helix: 0.90 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -2.25 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 182 TYR 0.026 0.001 TYR I 137 PHE 0.014 0.001 PHE D 114 TRP 0.025 0.001 TRP N 131 HIS 0.007 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00309 (11247) covalent geometry : angle 0.64347 (15262) hydrogen bonds : bond 0.02965 ( 528) hydrogen bonds : angle 4.24905 ( 1488) Misc. bond : bond 0.00550 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 0.439 Fit side-chains TARDY: cannot create tardy model for: "LEU A 112 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 133 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8999 (mt) REVERT: D 112 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6297 (tp) REVERT: D 139 LYS cc_start: 0.8245 (mppt) cc_final: 0.7973 (mmtm) REVERT: D 144 GLU cc_start: 0.8198 (tt0) cc_final: 0.7788 (tt0) REVERT: E 145 GLN cc_start: 0.9259 (mt0) cc_final: 0.9053 (mt0) REVERT: G 130 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8135 (mm-30) REVERT: G 134 ASP cc_start: 0.8520 (m-30) cc_final: 0.8124 (m-30) REVERT: G 194 ARG cc_start: 0.7360 (ttp80) cc_final: 0.6861 (ttp80) REVERT: H 134 ASP cc_start: 0.8242 (m-30) cc_final: 0.7989 (m-30) REVERT: I 194 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6578 (tmt-80) REVERT: J 112 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6462 (tm) REVERT: K 117 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: K 164 SER cc_start: 0.8866 (t) cc_final: 0.8568 (m) REVERT: L 182 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: L 193 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8254 (mt-10) REVERT: M 175 ASP cc_start: 0.8162 (p0) cc_final: 0.7858 (m-30) REVERT: N 122 LEU cc_start: 0.7329 (tt) cc_final: 0.7096 (tp) REVERT: N 158 LYS cc_start: 0.8458 (mttp) cc_final: 0.8155 (mttp) REVERT: O 152 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5275 (mt-10) outliers start: 17 outliers final: 12 residues processed: 259 average time/residue: 0.1301 time to fit residues: 45.5499 Evaluate side-chains 259 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain H residue 112 LEU 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 117 GLN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 152 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 124 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 108 optimal weight: 0.0570 chunk 8 optimal weight: 0.0060 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 GLN E 113 HIS G 117 GLN O 117 GLN O 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.119789 restraints weight = 14321.888| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.15 r_work: 0.3216 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 1.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11249 Z= 0.103 Angle : 0.605 12.090 15262 Z= 0.294 Chirality : 0.041 0.176 1679 Planarity : 0.004 0.037 1936 Dihedral : 4.764 49.152 1458 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.27 % Allowed : 17.08 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.24), residues: 1296 helix: 1.22 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.46 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 182 TYR 0.023 0.001 TYR I 137 PHE 0.014 0.001 PHE D 114 TRP 0.024 0.001 TRP N 131 HIS 0.007 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00240 (11247) covalent geometry : angle 0.60467 (15262) hydrogen bonds : bond 0.02617 ( 528) hydrogen bonds : angle 4.09680 ( 1488) Misc. bond : bond 0.00434 ( 2) =============================================================================== Job complete usr+sys time: 2671.18 seconds wall clock time: 46 minutes 47.55 seconds (2807.55 seconds total)