Starting phenix.real_space_refine on Mon Apr 6 16:32:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxt_64601/04_2026/9uxt_64601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxt_64601/04_2026/9uxt_64601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxt_64601/04_2026/9uxt_64601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxt_64601/04_2026/9uxt_64601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxt_64601/04_2026/9uxt_64601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxt_64601/04_2026/9uxt_64601.map" } resolution = 3.07 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.004 sd= 0.048 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 182 5.16 5 C 12642 2.51 5 N 3486 2.21 5 O 3682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19992 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "B" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "C" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "D" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "E" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "F" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "G" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "H" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "I" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "J" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "K" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "L" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "M" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "N" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1428 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Time building chain proxies: 4.49, per 1000 atoms: 0.22 Number of scatterers: 19992 At special positions: 0 Unit cell: (115.17, 113.076, 108.19, 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 182 16.00 O 3682 8.00 N 3486 7.00 C 12642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 730.2 milliseconds 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4732 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 42 sheets defined 44.7% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 13 through 30 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 108 through 133 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'B' and resid 13 through 30 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 74 through 81 Processing helix chain 'B' and resid 108 through 133 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 154 through 161 Processing helix chain 'C' and resid 13 through 30 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.535A pdb=" N GLY C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 108 through 133 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 45 through 58 removed outlier: 3.522A pdb=" N GLY D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 81 Processing helix chain 'D' and resid 108 through 133 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 154 through 161 Processing helix chain 'E' and resid 13 through 30 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 74 through 81 Processing helix chain 'E' and resid 108 through 133 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 13 through 30 Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 74 through 80 Processing helix chain 'F' and resid 108 through 133 Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 154 through 161 Processing helix chain 'G' and resid 13 through 30 Processing helix chain 'G' and resid 45 through 58 Processing helix chain 'G' and resid 74 through 80 Processing helix chain 'G' and resid 108 through 133 Processing helix chain 'G' and resid 141 through 148 Processing helix chain 'G' and resid 154 through 161 Processing helix chain 'H' and resid 13 through 30 Processing helix chain 'H' and resid 45 through 58 removed outlier: 3.526A pdb=" N GLY H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 81 Processing helix chain 'H' and resid 108 through 133 Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'H' and resid 154 through 161 Processing helix chain 'I' and resid 13 through 30 Processing helix chain 'I' and resid 45 through 58 removed outlier: 3.515A pdb=" N GLY I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 81 Processing helix chain 'I' and resid 108 through 133 Processing helix chain 'I' and resid 141 through 148 Processing helix chain 'I' and resid 154 through 161 Processing helix chain 'J' and resid 13 through 30 Processing helix chain 'J' and resid 45 through 58 Processing helix chain 'J' and resid 74 through 81 Processing helix chain 'J' and resid 108 through 133 Processing helix chain 'J' and resid 141 through 148 Processing helix chain 'J' and resid 154 through 161 Processing helix chain 'K' and resid 13 through 30 Processing helix chain 'K' and resid 45 through 58 Processing helix chain 'K' and resid 74 through 80 Processing helix chain 'K' and resid 108 through 133 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 154 through 161 Processing helix chain 'L' and resid 13 through 30 Processing helix chain 'L' and resid 45 through 58 Processing helix chain 'L' and resid 73 through 81 removed outlier: 4.202A pdb=" N ILE L 77 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 133 Processing helix chain 'L' and resid 141 through 148 Processing helix chain 'L' and resid 154 through 161 Processing helix chain 'M' and resid 13 through 30 Processing helix chain 'M' and resid 45 through 58 Processing helix chain 'M' and resid 74 through 80 Processing helix chain 'M' and resid 108 through 133 Processing helix chain 'M' and resid 141 through 148 Processing helix chain 'M' and resid 154 through 161 Processing helix chain 'N' and resid 13 through 30 Processing helix chain 'N' and resid 45 through 58 Processing helix chain 'N' and resid 74 through 81 Processing helix chain 'N' and resid 108 through 133 Processing helix chain 'N' and resid 141 through 148 Processing helix chain 'N' and resid 154 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.301A pdb=" N LEU A 94 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 71 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS A 84 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 166 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 87 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.301A pdb=" N LEU A 94 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 71 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N THR A 41 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N THR A 70 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 153 removed outlier: 8.358A pdb=" N LEU B 94 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 71 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 84 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 166 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 87 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 153 removed outlier: 8.358A pdb=" N LEU B 94 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 71 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR B 41 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR B 70 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.324A pdb=" N LEU C 94 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C 71 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS C 84 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 166 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 87 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.324A pdb=" N LEU C 94 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C 71 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR C 41 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR C 70 " --> pdb=" O THR C 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AB3, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=AB4, first strand: chain 'D' and resid 151 through 153 removed outlier: 8.368A pdb=" N LEU D 94 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 71 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 84 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 166 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 87 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 153 removed outlier: 8.368A pdb=" N LEU D 94 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 71 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR D 41 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR D 70 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'D' and resid 105 through 107 Processing sheet with id=AB8, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.419A pdb=" N LEU E 94 " --> pdb=" O GLY E 69 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 71 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS E 84 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 166 " --> pdb=" O ARG E 85 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 87 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.419A pdb=" N LEU E 94 " --> pdb=" O GLY E 69 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 71 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR E 41 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR E 70 " --> pdb=" O THR E 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AC2, first strand: chain 'E' and resid 105 through 107 Processing sheet with id=AC3, first strand: chain 'F' and resid 166 through 167 removed outlier: 3.575A pdb=" N ALA F 166 " --> pdb=" O ARG F 85 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 87 " --> pdb=" O ALA F 166 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS F 84 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 71 through 72 removed outlier: 6.742A pdb=" N VAL F 71 " --> pdb=" O LEU F 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC6, first strand: chain 'F' and resid 105 through 107 Processing sheet with id=AC7, first strand: chain 'G' and resid 151 through 153 removed outlier: 8.414A pdb=" N LEU G 94 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL G 71 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS G 84 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G 166 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 87 " --> pdb=" O ALA G 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 151 through 153 removed outlier: 8.414A pdb=" N LEU G 94 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL G 71 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N THR G 41 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR G 70 " --> pdb=" O THR G 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=AD1, first strand: chain 'G' and resid 105 through 107 Processing sheet with id=AD2, first strand: chain 'H' and resid 151 through 153 removed outlier: 8.341A pdb=" N LEU H 94 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL H 71 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS H 84 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA H 166 " --> pdb=" O ARG H 85 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 87 " --> pdb=" O ALA H 166 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 151 through 153 removed outlier: 8.341A pdb=" N LEU H 94 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL H 71 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR H 41 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR H 70 " --> pdb=" O THR H 41 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 151 through 153 removed outlier: 8.367A pdb=" N LEU I 94 " --> pdb=" O GLY I 69 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL I 71 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS I 84 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA I 166 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA I 87 " --> pdb=" O ALA I 166 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 151 through 153 removed outlier: 8.367A pdb=" N LEU I 94 " --> pdb=" O GLY I 69 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL I 71 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR I 41 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N THR I 70 " --> pdb=" O THR I 41 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 151 through 153 removed outlier: 8.314A pdb=" N LEU J 94 " --> pdb=" O GLY J 69 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 71 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS J 84 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA J 166 " --> pdb=" O ARG J 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA J 87 " --> pdb=" O ALA J 166 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 151 through 153 removed outlier: 8.314A pdb=" N LEU J 94 " --> pdb=" O GLY J 69 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 71 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N THR J 41 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N THR J 70 " --> pdb=" O THR J 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 151 through 153 removed outlier: 8.383A pdb=" N LEU K 94 " --> pdb=" O GLY K 69 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL K 71 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS K 84 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA K 166 " --> pdb=" O ARG K 85 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA K 87 " --> pdb=" O ALA K 166 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 151 through 153 removed outlier: 8.383A pdb=" N LEU K 94 " --> pdb=" O GLY K 69 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL K 71 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N THR K 41 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR K 70 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 151 through 153 removed outlier: 8.342A pdb=" N LEU L 94 " --> pdb=" O GLY L 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL L 71 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU L 63 " --> pdb=" O HIS L 84 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR L 86 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR L 65 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA L 166 " --> pdb=" O ARG L 85 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA L 87 " --> pdb=" O ALA L 166 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 151 through 153 removed outlier: 8.342A pdb=" N LEU L 94 " --> pdb=" O GLY L 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL L 71 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR L 41 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR L 70 " --> pdb=" O THR L 41 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 151 through 153 removed outlier: 8.321A pdb=" N LEU M 94 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL M 71 " --> pdb=" O LEU M 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS M 84 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA M 166 " --> pdb=" O ARG M 85 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 87 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 151 through 153 removed outlier: 8.321A pdb=" N LEU M 94 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL M 71 " --> pdb=" O LEU M 94 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR M 41 " --> pdb=" O LEU M 68 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR M 70 " --> pdb=" O THR M 41 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 151 through 153 removed outlier: 8.338A pdb=" N LEU N 94 " --> pdb=" O GLY N 69 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL N 71 " --> pdb=" O LEU N 94 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS N 84 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA N 166 " --> pdb=" O ARG N 85 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA N 87 " --> pdb=" O ALA N 166 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 151 through 153 removed outlier: 8.338A pdb=" N LEU N 94 " --> pdb=" O GLY N 69 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL N 71 " --> pdb=" O LEU N 94 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR N 41 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR N 70 " --> pdb=" O THR N 41 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3402 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: 3.64 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6664 1.34 - 1.46: 4219 1.46 - 1.57: 9305 1.57 - 1.69: 0 1.69 - 1.81: 308 Bond restraints: 20496 Sorted by residual: bond pdb=" N TYR C 149 " pdb=" CA TYR C 149 " ideal model delta sigma weight residual 1.463 1.453 0.011 1.08e-02 8.57e+03 9.85e-01 bond pdb=" CG LEU K 153 " pdb=" CD2 LEU K 153 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.71e-01 bond pdb=" CG LEU I 153 " pdb=" CD2 LEU I 153 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.68e-01 bond pdb=" CG LEU A 153 " pdb=" CD2 LEU A 153 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.37e-01 bond pdb=" CB ASP M 33 " pdb=" CG ASP M 33 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.34e-01 ... (remaining 20491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 26336 1.02 - 2.05: 1176 2.05 - 3.07: 248 3.07 - 4.10: 41 4.10 - 5.12: 31 Bond angle restraints: 27832 Sorted by residual: angle pdb=" N HIS B 96 " pdb=" CA HIS B 96 " pdb=" C HIS B 96 " ideal model delta sigma weight residual 108.22 110.03 -1.81 9.00e-01 1.23e+00 4.02e+00 angle pdb=" C GLY F 43 " pdb=" N GLY F 44 " pdb=" CA GLY F 44 " ideal model delta sigma weight residual 121.83 119.60 2.23 1.19e+00 7.06e-01 3.50e+00 angle pdb=" N HIS N 96 " pdb=" CA HIS N 96 " pdb=" C HIS N 96 " ideal model delta sigma weight residual 108.22 109.85 -1.63 9.00e-01 1.23e+00 3.29e+00 angle pdb=" N GLU N 157 " pdb=" CA GLU N 157 " pdb=" C GLU N 157 " ideal model delta sigma weight residual 113.01 110.84 2.17 1.20e+00 6.94e-01 3.27e+00 angle pdb=" CA ASP M 33 " pdb=" CB ASP M 33 " pdb=" CG ASP M 33 " ideal model delta sigma weight residual 112.60 114.38 -1.78 1.00e+00 1.00e+00 3.18e+00 ... (remaining 27827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 11035 14.73 - 29.46: 794 29.46 - 44.20: 182 44.20 - 58.93: 42 58.93 - 73.66: 15 Dihedral angle restraints: 12068 sinusoidal: 4676 harmonic: 7392 Sorted by residual: dihedral pdb=" CA ALA C 148 " pdb=" C ALA C 148 " pdb=" N TYR C 149 " pdb=" CA TYR C 149 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU H 45 " pdb=" C GLU H 45 " pdb=" N CYS H 46 " pdb=" CA CYS H 46 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ALA L 148 " pdb=" C ALA L 148 " pdb=" N TYR L 149 " pdb=" CA TYR L 149 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 12065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1853 0.025 - 0.051: 759 0.051 - 0.076: 230 0.076 - 0.102: 140 0.102 - 0.127: 84 Chirality restraints: 3066 Sorted by residual: chirality pdb=" CA VAL G 71 " pdb=" N VAL G 71 " pdb=" C VAL G 71 " pdb=" CB VAL G 71 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL F 71 " pdb=" N VAL F 71 " pdb=" C VAL F 71 " pdb=" CB VAL F 71 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL L 71 " pdb=" N VAL L 71 " pdb=" C VAL L 71 " pdb=" CB VAL L 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 3063 not shown) Planarity restraints: 3598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 149 " 0.004 2.00e-02 2.50e+03 8.06e-03 1.30e+00 pdb=" CG TYR E 149 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 149 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 149 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR E 149 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 149 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 149 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 149 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 149 " 0.005 2.00e-02 2.50e+03 7.15e-03 1.02e+00 pdb=" CG TYR N 149 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR N 149 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR N 149 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR N 149 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR N 149 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR N 149 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 149 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR F 149 " 0.015 5.00e-02 4.00e+02 2.34e-02 8.76e-01 pdb=" N PRO F 150 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO F 150 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 150 " 0.013 5.00e-02 4.00e+02 ... (remaining 3595 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5115 2.81 - 3.33: 19190 3.33 - 3.86: 34009 3.86 - 4.38: 37544 4.38 - 4.90: 69143 Nonbonded interactions: 165001 Sorted by model distance: nonbonded pdb=" NH2 ARG A 110 " pdb=" OD1 ASP J 107 " model vdw 2.288 3.120 nonbonded pdb=" OD1 ASP C 107 " pdb=" NH2 ARG H 110 " model vdw 2.297 3.120 nonbonded pdb=" OE1 GLU A 131 " pdb=" NH2 ARG G 90 " model vdw 2.302 3.120 nonbonded pdb=" NH2 ARG D 110 " pdb=" OD1 ASP N 107 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASP E 107 " pdb=" NH2 ARG M 110 " model vdw 2.305 3.120 ... (remaining 164996 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 18.080 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 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 : 0.003 0.033 20496 Z= 0.148 Angle : 0.526 5.123 27832 Z= 0.281 Chirality : 0.038 0.127 3066 Planarity : 0.003 0.023 3598 Dihedral : 11.423 73.659 7336 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.17), residues: 2534 helix: 2.77 (0.15), residues: 1134 sheet: 1.03 (0.26), residues: 462 loop : -0.43 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 151 TYR 0.019 0.002 TYR E 149 PHE 0.011 0.001 PHE K 79 TRP 0.004 0.001 TRP G 179 HIS 0.005 0.001 HIS G 7 Details of bonding type rmsd covalent geometry : bond 0.00323 (20496) covalent geometry : angle 0.52634 (27832) hydrogen bonds : bond 0.15427 ( 1137) hydrogen bonds : angle 5.52958 ( 3402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 0.685 Fit side-chains REVERT: A 30 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6584 (mp10) REVERT: A 111 MET cc_start: 0.6712 (mmm) cc_final: 0.6225 (mmm) REVERT: A 147 MET cc_start: 0.7291 (tpt) cc_final: 0.7044 (tpt) REVERT: B 30 GLN cc_start: 0.6943 (mm-40) cc_final: 0.6348 (mp10) REVERT: B 65 THR cc_start: 0.7001 (p) cc_final: 0.6501 (t) REVERT: B 74 MET cc_start: 0.7673 (mmm) cc_final: 0.7310 (mmm) REVERT: B 147 MET cc_start: 0.7184 (tpt) cc_final: 0.6814 (tpt) REVERT: C 65 THR cc_start: 0.7078 (p) cc_final: 0.6735 (p) REVERT: C 74 MET cc_start: 0.7796 (mmm) cc_final: 0.7579 (mmm) REVERT: C 147 MET cc_start: 0.7172 (tpt) cc_final: 0.6864 (tpt) REVERT: D 16 THR cc_start: 0.7046 (m) cc_final: 0.6700 (p) REVERT: D 30 GLN cc_start: 0.7148 (mm-40) cc_final: 0.6631 (mp10) REVERT: D 65 THR cc_start: 0.6970 (p) cc_final: 0.6639 (p) REVERT: D 92 LYS cc_start: 0.7673 (ptpp) cc_final: 0.7259 (pttm) REVERT: D 147 MET cc_start: 0.7259 (tpt) cc_final: 0.7007 (tpt) REVERT: E 30 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6559 (mp10) REVERT: E 74 MET cc_start: 0.7927 (mmm) cc_final: 0.7679 (mmm) REVERT: E 92 LYS cc_start: 0.7837 (pttp) cc_final: 0.7595 (pttt) REVERT: E 102 LEU cc_start: 0.6454 (tp) cc_final: 0.6198 (tp) REVERT: E 147 MET cc_start: 0.7308 (tpt) cc_final: 0.6884 (tpt) REVERT: F 4 HIS cc_start: 0.7133 (m-70) cc_final: 0.6688 (m-70) REVERT: F 30 GLN cc_start: 0.6841 (mm-40) cc_final: 0.6274 (mp10) REVERT: F 65 THR cc_start: 0.7075 (p) cc_final: 0.6731 (p) REVERT: F 102 LEU cc_start: 0.6878 (tt) cc_final: 0.6341 (tt) REVERT: F 147 MET cc_start: 0.6905 (tpt) cc_final: 0.6638 (tpt) REVERT: G 30 GLN cc_start: 0.6868 (mm-40) cc_final: 0.6409 (mp10) REVERT: G 147 MET cc_start: 0.7079 (tpt) cc_final: 0.6692 (tpt) REVERT: H 30 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6377 (mp10) REVERT: H 74 MET cc_start: 0.7744 (mmm) cc_final: 0.7501 (mmm) REVERT: H 147 MET cc_start: 0.6844 (tpt) cc_final: 0.6614 (tpt) REVERT: H 163 MET cc_start: 0.6763 (mmm) cc_final: 0.6377 (mmm) REVERT: I 30 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6503 (mp10) REVERT: I 65 THR cc_start: 0.7100 (p) cc_final: 0.6833 (p) REVERT: I 111 MET cc_start: 0.6997 (mmm) cc_final: 0.6436 (mmm) REVERT: I 147 MET cc_start: 0.7242 (tpt) cc_final: 0.6971 (tpt) REVERT: J 30 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6423 (mp10) REVERT: J 65 THR cc_start: 0.6986 (p) cc_final: 0.6712 (p) REVERT: J 147 MET cc_start: 0.7143 (tpt) cc_final: 0.6851 (tpt) REVERT: K 4 HIS cc_start: 0.6882 (m-70) cc_final: 0.6514 (m-70) REVERT: K 30 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6539 (mp10) REVERT: K 92 LYS cc_start: 0.7926 (pttp) cc_final: 0.7581 (pttm) REVERT: K 102 LEU cc_start: 0.6385 (tt) cc_final: 0.5949 (tt) REVERT: K 111 MET cc_start: 0.7038 (mmm) cc_final: 0.6732 (mmm) REVERT: K 147 MET cc_start: 0.6906 (tpt) cc_final: 0.6671 (tpt) REVERT: L 30 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6527 (mp10) REVERT: L 92 LYS cc_start: 0.7762 (ptpp) cc_final: 0.7509 (ptpt) REVERT: L 102 LEU cc_start: 0.6531 (tt) cc_final: 0.6200 (tt) REVERT: L 111 MET cc_start: 0.6882 (mmm) cc_final: 0.6584 (mmm) REVERT: L 147 MET cc_start: 0.6720 (tpt) cc_final: 0.6477 (tpt) REVERT: M 4 HIS cc_start: 0.6881 (m-70) cc_final: 0.6642 (m-70) REVERT: M 30 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6424 (mp10) REVERT: M 65 THR cc_start: 0.6938 (p) cc_final: 0.6654 (p) REVERT: M 102 LEU cc_start: 0.7097 (tp) cc_final: 0.6878 (tp) REVERT: M 147 MET cc_start: 0.7230 (tpt) cc_final: 0.6944 (tpt) REVERT: N 30 GLN cc_start: 0.6760 (mm-40) cc_final: 0.6329 (mp10) REVERT: N 65 THR cc_start: 0.7043 (p) cc_final: 0.6816 (p) REVERT: N 74 MET cc_start: 0.7632 (mmm) cc_final: 0.7297 (mmm) REVERT: N 92 LYS cc_start: 0.7759 (ptpp) cc_final: 0.7519 (pttt) REVERT: N 141 ASP cc_start: 0.5167 (t70) cc_final: 0.4900 (t70) REVERT: N 147 MET cc_start: 0.7212 (tpt) cc_final: 0.6919 (tpt) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.1110 time to fit residues: 87.9828 Evaluate side-chains 429 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 0.0770 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 96 HIS ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 HIS ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS H 96 HIS I 7 HIS ** I 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 HIS ** M 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.149318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136760 restraints weight = 26769.309| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.45 r_work: 0.3635 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20496 Z= 0.112 Angle : 0.533 7.956 27832 Z= 0.261 Chirality : 0.040 0.152 3066 Planarity : 0.003 0.031 3598 Dihedral : 3.824 14.720 2786 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.47 % Allowed : 8.94 % Favored : 89.59 % 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 are not related in a simple way. whole: 2.03 (0.17), residues: 2534 helix: 2.77 (0.15), residues: 1148 sheet: 1.03 (0.24), residues: 462 loop : -0.34 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 110 TYR 0.020 0.002 TYR K 125 PHE 0.009 0.001 PHE K 79 TRP 0.003 0.000 TRP A 179 HIS 0.007 0.001 HIS I 4 Details of bonding type rmsd covalent geometry : bond 0.00239 (20496) covalent geometry : angle 0.53316 (27832) hydrogen bonds : bond 0.03501 ( 1137) hydrogen bonds : angle 4.09105 ( 3402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 462 time to evaluate : 0.638 Fit side-chains REVERT: A 30 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7451 (mp10) REVERT: A 92 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8220 (mtmm) REVERT: A 125 TYR cc_start: 0.8632 (t80) cc_final: 0.8411 (t80) REVERT: B 30 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7311 (mp10) REVERT: B 65 THR cc_start: 0.7623 (p) cc_final: 0.7412 (p) REVERT: B 125 TYR cc_start: 0.8616 (t80) cc_final: 0.8281 (t80) REVERT: C 30 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7313 (mm-40) REVERT: C 147 MET cc_start: 0.7625 (tpt) cc_final: 0.7424 (tpt) REVERT: C 179 TRP cc_start: 0.7914 (m100) cc_final: 0.7632 (m100) REVERT: D 16 THR cc_start: 0.8170 (m) cc_final: 0.7807 (p) REVERT: D 30 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7525 (mm-40) REVERT: D 74 MET cc_start: 0.7824 (mmm) cc_final: 0.7237 (mmm) REVERT: D 92 LYS cc_start: 0.8406 (ptpp) cc_final: 0.8045 (pttm) REVERT: E 30 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7341 (mm-40) REVERT: E 147 MET cc_start: 0.7853 (tpt) cc_final: 0.7599 (tpt) REVERT: E 170 MET cc_start: 0.8252 (mmm) cc_final: 0.7968 (tpp) REVERT: F 30 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7198 (mp10) REVERT: F 147 MET cc_start: 0.7612 (tpt) cc_final: 0.7284 (mmm) REVERT: F 179 TRP cc_start: 0.7860 (m100) cc_final: 0.7404 (m100) REVERT: G 74 MET cc_start: 0.8007 (mmm) cc_final: 0.7687 (mmm) REVERT: G 147 MET cc_start: 0.7819 (tpt) cc_final: 0.7509 (tpt) REVERT: H 111 MET cc_start: 0.8108 (mmm) cc_final: 0.7835 (mmm) REVERT: H 147 MET cc_start: 0.7509 (tpt) cc_final: 0.7266 (tpt) REVERT: H 163 MET cc_start: 0.7260 (mmm) cc_final: 0.7014 (mmm) REVERT: H 170 MET cc_start: 0.8440 (tpp) cc_final: 0.8066 (mmm) REVERT: H 179 TRP cc_start: 0.7941 (m100) cc_final: 0.7619 (m100) REVERT: I 65 THR cc_start: 0.7704 (p) cc_final: 0.7400 (p) REVERT: I 179 TRP cc_start: 0.7920 (m100) cc_final: 0.7382 (m100) REVERT: J 16 THR cc_start: 0.8233 (m) cc_final: 0.7974 (p) REVERT: J 92 LYS cc_start: 0.8605 (pttt) cc_final: 0.8363 (ptpt) REVERT: J 147 MET cc_start: 0.7816 (tpt) cc_final: 0.7559 (tpt) REVERT: L 92 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8351 (ptpt) REVERT: L 111 MET cc_start: 0.8107 (mmm) cc_final: 0.7798 (mmm) REVERT: L 147 MET cc_start: 0.7346 (tpt) cc_final: 0.7101 (tpt) REVERT: M 65 THR cc_start: 0.7484 (p) cc_final: 0.7241 (p) REVERT: M 147 MET cc_start: 0.7926 (tpt) cc_final: 0.7696 (tpt) REVERT: N 74 MET cc_start: 0.7836 (mmm) cc_final: 0.7609 (mmm) REVERT: N 147 MET cc_start: 0.7672 (tpt) cc_final: 0.7380 (tpt) REVERT: N 170 MET cc_start: 0.8578 (tpp) cc_final: 0.8290 (tpp) outliers start: 31 outliers final: 15 residues processed: 471 average time/residue: 0.1077 time to fit residues: 85.0058 Evaluate side-chains 454 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 438 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 181 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 155 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS B 4 HIS B 96 HIS B 156 GLN C 4 HIS C 96 HIS ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 96 HIS E 4 HIS ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 HIS ** I 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 HIS J 182 HIS ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN L 4 HIS ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122411 restraints weight = 26568.053| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.33 r_work: 0.3426 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20496 Z= 0.243 Angle : 0.604 9.270 27832 Z= 0.304 Chirality : 0.043 0.190 3066 Planarity : 0.004 0.033 3598 Dihedral : 4.307 18.228 2786 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.74 % Allowed : 12.25 % Favored : 84.01 % 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 are not related in a simple way. whole: 1.46 (0.16), residues: 2534 helix: 2.34 (0.15), residues: 1204 sheet: 0.21 (0.18), residues: 616 loop : -0.71 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 151 TYR 0.021 0.002 TYR H 125 PHE 0.028 0.002 PHE C 93 TRP 0.010 0.001 TRP B 179 HIS 0.008 0.002 HIS N 4 Details of bonding type rmsd covalent geometry : bond 0.00553 (20496) covalent geometry : angle 0.60450 (27832) hydrogen bonds : bond 0.04406 ( 1137) hydrogen bonds : angle 4.15950 ( 3402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 339 time to evaluate : 0.545 Fit side-chains REVERT: A 92 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8690 (mtmm) REVERT: A 111 MET cc_start: 0.8345 (mmm) cc_final: 0.7928 (mmm) REVERT: A 163 MET cc_start: 0.8262 (mmm) cc_final: 0.7630 (mmm) REVERT: B 30 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7577 (mp10) REVERT: B 163 MET cc_start: 0.8294 (mtp) cc_final: 0.7811 (mmm) REVERT: C 6 ILE cc_start: 0.8043 (mt) cc_final: 0.7808 (mt) REVERT: C 16 THR cc_start: 0.8678 (m) cc_final: 0.8319 (p) REVERT: C 51 THR cc_start: 0.8427 (m) cc_final: 0.8226 (m) REVERT: C 147 MET cc_start: 0.8184 (tpt) cc_final: 0.7881 (tpt) REVERT: D 74 MET cc_start: 0.7947 (mmm) cc_final: 0.7413 (mmm) REVERT: D 92 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8510 (ptpp) REVERT: E 6 ILE cc_start: 0.8253 (mt) cc_final: 0.8004 (mt) REVERT: E 94 LEU cc_start: 0.8563 (tt) cc_final: 0.8352 (tp) REVERT: E 147 MET cc_start: 0.8212 (tpt) cc_final: 0.7870 (tpt) REVERT: E 170 MET cc_start: 0.8626 (mmm) cc_final: 0.8296 (tpp) REVERT: F 6 ILE cc_start: 0.8106 (mt) cc_final: 0.7852 (mt) REVERT: F 16 THR cc_start: 0.8522 (m) cc_final: 0.8204 (p) REVERT: F 147 MET cc_start: 0.8126 (tpt) cc_final: 0.7806 (tpt) REVERT: G 65 THR cc_start: 0.7550 (p) cc_final: 0.7234 (p) REVERT: G 74 MET cc_start: 0.8352 (mmm) cc_final: 0.8061 (mmm) REVERT: G 147 MET cc_start: 0.8168 (tpt) cc_final: 0.7967 (tpp) REVERT: H 163 MET cc_start: 0.8154 (mmm) cc_final: 0.7456 (mmm) REVERT: H 170 MET cc_start: 0.8852 (tpp) cc_final: 0.8379 (mmm) REVERT: I 16 THR cc_start: 0.8627 (m) cc_final: 0.8264 (p) REVERT: I 65 THR cc_start: 0.7785 (p) cc_final: 0.7451 (p) REVERT: I 90 ARG cc_start: 0.8536 (mpt90) cc_final: 0.8316 (mmt180) REVERT: J 147 MET cc_start: 0.8220 (tpt) cc_final: 0.7871 (tpt) REVERT: K 94 LEU cc_start: 0.8635 (tt) cc_final: 0.8412 (tp) REVERT: L 30 GLN cc_start: 0.8010 (mp10) cc_final: 0.7792 (mp10) REVERT: L 111 MET cc_start: 0.8317 (mmm) cc_final: 0.7873 (mmm) REVERT: L 147 MET cc_start: 0.7877 (tpt) cc_final: 0.7584 (tpt) REVERT: M 65 THR cc_start: 0.7518 (p) cc_final: 0.7269 (p) REVERT: M 94 LEU cc_start: 0.8595 (tt) cc_final: 0.8390 (tp) REVERT: M 147 MET cc_start: 0.8289 (tpt) cc_final: 0.8027 (tpt) REVERT: N 6 ILE cc_start: 0.8140 (mt) cc_final: 0.7938 (mt) REVERT: N 8 PHE cc_start: 0.8567 (t80) cc_final: 0.8304 (t80) REVERT: N 147 MET cc_start: 0.7951 (tpt) cc_final: 0.7684 (tpt) outliers start: 79 outliers final: 25 residues processed: 391 average time/residue: 0.1163 time to fit residues: 74.3239 Evaluate side-chains 357 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 331 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 152 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 179 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 187 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS ** D 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 HIS ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 HIS I 96 HIS J 4 HIS K 96 HIS ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 HIS N 96 HIS N 178 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121627 restraints weight = 26742.333| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.38 r_work: 0.3446 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20496 Z= 0.124 Angle : 0.478 8.235 27832 Z= 0.238 Chirality : 0.040 0.140 3066 Planarity : 0.003 0.026 3598 Dihedral : 4.033 19.159 2786 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.98 % Allowed : 13.67 % Favored : 83.35 % 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 are not related in a simple way. whole: 1.46 (0.16), residues: 2534 helix: 2.65 (0.15), residues: 1190 sheet: -0.11 (0.20), residues: 504 loop : -0.84 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 144 TYR 0.019 0.002 TYR F 125 PHE 0.010 0.001 PHE C 93 TRP 0.006 0.000 TRP N 179 HIS 0.006 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00283 (20496) covalent geometry : angle 0.47843 (27832) hydrogen bonds : bond 0.03146 ( 1137) hydrogen bonds : angle 3.95070 ( 3402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 352 time to evaluate : 0.660 Fit side-chains REVERT: A 92 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8690 (mtmm) REVERT: A 163 MET cc_start: 0.8132 (mmm) cc_final: 0.7537 (mmm) REVERT: B 78 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 163 MET cc_start: 0.8252 (mtp) cc_final: 0.7933 (mmm) REVERT: C 16 THR cc_start: 0.8615 (m) cc_final: 0.8293 (p) REVERT: C 80 LEU cc_start: 0.8073 (mt) cc_final: 0.7724 (mp) REVERT: C 125 TYR cc_start: 0.8764 (t80) cc_final: 0.8319 (t80) REVERT: C 147 MET cc_start: 0.8085 (tpt) cc_final: 0.7816 (tpt) REVERT: D 74 MET cc_start: 0.7932 (mmm) cc_final: 0.7626 (mmm) REVERT: D 102 LEU cc_start: 0.8024 (tt) cc_final: 0.7641 (tt) REVERT: E 6 ILE cc_start: 0.8048 (mt) cc_final: 0.7821 (mt) REVERT: E 94 LEU cc_start: 0.8556 (tt) cc_final: 0.8326 (tp) REVERT: E 147 MET cc_start: 0.8086 (tpt) cc_final: 0.7781 (tpt) REVERT: E 170 MET cc_start: 0.8590 (mmm) cc_final: 0.8221 (tpp) REVERT: F 16 THR cc_start: 0.8496 (m) cc_final: 0.8213 (p) REVERT: F 74 MET cc_start: 0.8215 (mmm) cc_final: 0.7775 (mmm) REVERT: F 147 MET cc_start: 0.8045 (tpt) cc_final: 0.7718 (tpt) REVERT: G 16 THR cc_start: 0.8527 (m) cc_final: 0.8273 (p) REVERT: G 65 THR cc_start: 0.7492 (p) cc_final: 0.7181 (p) REVERT: G 147 MET cc_start: 0.8066 (tpt) cc_final: 0.7763 (tpt) REVERT: H 4 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7566 (m-70) REVERT: H 147 MET cc_start: 0.7884 (tpt) cc_final: 0.7532 (tpt) REVERT: H 163 MET cc_start: 0.8171 (mmm) cc_final: 0.7499 (mmm) REVERT: H 170 MET cc_start: 0.8856 (tpp) cc_final: 0.8377 (mmm) REVERT: I 16 THR cc_start: 0.8557 (m) cc_final: 0.8242 (p) REVERT: I 65 THR cc_start: 0.7736 (p) cc_final: 0.7405 (p) REVERT: I 90 ARG cc_start: 0.8526 (mpt90) cc_final: 0.8298 (mmt180) REVERT: J 16 THR cc_start: 0.8604 (m) cc_final: 0.8268 (p) REVERT: J 30 GLN cc_start: 0.8076 (mp10) cc_final: 0.7820 (mp10) REVERT: J 147 MET cc_start: 0.8160 (tpt) cc_final: 0.7777 (tpt) REVERT: J 163 MET cc_start: 0.8170 (mtp) cc_final: 0.7727 (mtp) REVERT: K 30 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: K 63 LEU cc_start: 0.7993 (tp) cc_final: 0.7773 (tp) REVERT: K 94 LEU cc_start: 0.8591 (tt) cc_final: 0.8342 (tp) REVERT: K 170 MET cc_start: 0.8877 (mmp) cc_final: 0.8547 (tpp) REVERT: L 6 ILE cc_start: 0.7797 (mt) cc_final: 0.7593 (mt) REVERT: L 111 MET cc_start: 0.8294 (mmm) cc_final: 0.7858 (mmm) REVERT: L 147 MET cc_start: 0.7822 (tpt) cc_final: 0.7535 (tpt) REVERT: M 147 MET cc_start: 0.8205 (tpt) cc_final: 0.7962 (tpt) REVERT: N 147 MET cc_start: 0.7955 (tpt) cc_final: 0.7670 (tpt) outliers start: 63 outliers final: 30 residues processed: 389 average time/residue: 0.1143 time to fit residues: 73.2483 Evaluate side-chains 382 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 348 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 137 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS B 4 HIS B 30 GLN C 67 ASN D 4 HIS E 4 HIS G 4 HIS ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123824 restraints weight = 26746.230| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.36 r_work: 0.3448 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20496 Z= 0.115 Angle : 0.458 6.831 27832 Z= 0.228 Chirality : 0.040 0.141 3066 Planarity : 0.003 0.026 3598 Dihedral : 3.946 20.216 2786 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.41 % Allowed : 14.05 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2534 helix: 2.64 (0.15), residues: 1204 sheet: -0.16 (0.20), residues: 504 loop : -0.67 (0.18), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 144 TYR 0.020 0.001 TYR A 125 PHE 0.008 0.001 PHE C 93 TRP 0.005 0.000 TRP F 179 HIS 0.016 0.001 HIS H 4 Details of bonding type rmsd covalent geometry : bond 0.00263 (20496) covalent geometry : angle 0.45834 (27832) hydrogen bonds : bond 0.02934 ( 1137) hydrogen bonds : angle 3.87261 ( 3402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 352 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8506 (pttt) REVERT: A 163 MET cc_start: 0.8122 (mmm) cc_final: 0.7510 (mmm) REVERT: B 163 MET cc_start: 0.8273 (mtp) cc_final: 0.7960 (mmm) REVERT: C 16 THR cc_start: 0.8559 (m) cc_final: 0.8317 (p) REVERT: C 80 LEU cc_start: 0.8068 (mt) cc_final: 0.7688 (mp) REVERT: C 147 MET cc_start: 0.8056 (tpt) cc_final: 0.7804 (tpt) REVERT: D 74 MET cc_start: 0.7879 (mmm) cc_final: 0.7558 (mmm) REVERT: D 102 LEU cc_start: 0.7992 (tt) cc_final: 0.7711 (tt) REVERT: E 6 ILE cc_start: 0.8014 (mt) cc_final: 0.7795 (mt) REVERT: E 94 LEU cc_start: 0.8530 (tt) cc_final: 0.8298 (tp) REVERT: E 147 MET cc_start: 0.8057 (tpt) cc_final: 0.7766 (tpt) REVERT: F 16 THR cc_start: 0.8481 (m) cc_final: 0.8213 (p) REVERT: F 74 MET cc_start: 0.8258 (mmm) cc_final: 0.7802 (mmm) REVERT: F 147 MET cc_start: 0.8018 (tpt) cc_final: 0.7694 (tpt) REVERT: G 16 THR cc_start: 0.8513 (m) cc_final: 0.8270 (p) REVERT: G 65 THR cc_start: 0.7519 (p) cc_final: 0.7203 (p) REVERT: G 147 MET cc_start: 0.8020 (tpt) cc_final: 0.7731 (tpt) REVERT: H 23 THR cc_start: 0.7851 (m) cc_final: 0.7621 (p) REVERT: H 65 THR cc_start: 0.7753 (p) cc_final: 0.7455 (p) REVERT: H 74 MET cc_start: 0.7918 (mmm) cc_final: 0.7247 (mmm) REVERT: H 147 MET cc_start: 0.7849 (tpt) cc_final: 0.7544 (tpt) REVERT: H 163 MET cc_start: 0.8170 (mmm) cc_final: 0.7463 (mmm) REVERT: H 170 MET cc_start: 0.8867 (tpp) cc_final: 0.8420 (mmm) REVERT: I 65 THR cc_start: 0.7757 (p) cc_final: 0.7410 (p) REVERT: I 90 ARG cc_start: 0.8522 (mpt90) cc_final: 0.8292 (mmt180) REVERT: J 16 THR cc_start: 0.8582 (m) cc_final: 0.8260 (p) REVERT: J 147 MET cc_start: 0.8120 (tpt) cc_final: 0.7762 (tpt) REVERT: J 163 MET cc_start: 0.8113 (mtp) cc_final: 0.7349 (mmm) REVERT: K 94 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8344 (tp) REVERT: L 30 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: L 111 MET cc_start: 0.8257 (mmm) cc_final: 0.7824 (mmm) REVERT: L 147 MET cc_start: 0.7822 (tpt) cc_final: 0.7538 (tpt) REVERT: M 147 MET cc_start: 0.8219 (tpt) cc_final: 0.7983 (tpt) REVERT: N 147 MET cc_start: 0.7943 (tpt) cc_final: 0.7659 (tpt) outliers start: 72 outliers final: 42 residues processed: 396 average time/residue: 0.1155 time to fit residues: 75.1534 Evaluate side-chains 392 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 347 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain N residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 247 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS A 182 HIS B 4 HIS C 4 HIS D 4 HIS E 4 HIS E 182 HIS ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 HIS H 182 HIS I 4 HIS J 4 HIS ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 HIS N 182 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120141 restraints weight = 26912.725| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.40 r_work: 0.3393 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20496 Z= 0.234 Angle : 0.534 8.131 27832 Z= 0.271 Chirality : 0.043 0.178 3066 Planarity : 0.003 0.027 3598 Dihedral : 4.247 22.409 2786 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.59 % Allowed : 13.91 % Favored : 81.50 % 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 are not related in a simple way. whole: 1.30 (0.16), residues: 2534 helix: 2.58 (0.15), residues: 1204 sheet: -0.60 (0.20), residues: 504 loop : -0.78 (0.18), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 85 TYR 0.028 0.002 TYR A 125 PHE 0.014 0.002 PHE C 93 TRP 0.005 0.001 TRP F 179 HIS 0.007 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00537 (20496) covalent geometry : angle 0.53397 (27832) hydrogen bonds : bond 0.03798 ( 1137) hydrogen bonds : angle 4.14827 ( 3402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 339 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: B 30 GLN cc_start: 0.8001 (mp10) cc_final: 0.7365 (mp10) REVERT: B 163 MET cc_start: 0.8357 (mtp) cc_final: 0.7972 (mmm) REVERT: C 16 THR cc_start: 0.8627 (m) cc_final: 0.8344 (p) REVERT: C 147 MET cc_start: 0.8142 (tpt) cc_final: 0.7883 (tpt) REVERT: D 92 LYS cc_start: 0.8871 (pttt) cc_final: 0.8494 (pttm) REVERT: E 6 ILE cc_start: 0.8090 (mt) cc_final: 0.7853 (mt) REVERT: E 35 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8192 (mp) REVERT: E 94 LEU cc_start: 0.8564 (tt) cc_final: 0.8345 (tp) REVERT: E 147 MET cc_start: 0.8198 (tpt) cc_final: 0.7919 (tpt) REVERT: F 6 ILE cc_start: 0.8009 (mt) cc_final: 0.7803 (mt) REVERT: F 16 THR cc_start: 0.8513 (m) cc_final: 0.8266 (p) REVERT: F 74 MET cc_start: 0.8418 (mmm) cc_final: 0.7908 (mmm) REVERT: F 147 MET cc_start: 0.8191 (tpt) cc_final: 0.7857 (tpt) REVERT: G 16 THR cc_start: 0.8509 (m) cc_final: 0.8256 (p) REVERT: G 65 THR cc_start: 0.7656 (p) cc_final: 0.7335 (p) REVERT: G 147 MET cc_start: 0.8197 (tpt) cc_final: 0.7897 (tpt) REVERT: H 59 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7917 (mp) REVERT: H 147 MET cc_start: 0.7981 (tpt) cc_final: 0.7654 (tpt) REVERT: H 172 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7526 (mp) REVERT: I 16 THR cc_start: 0.8524 (m) cc_final: 0.8217 (p) REVERT: I 65 THR cc_start: 0.7858 (p) cc_final: 0.7578 (p) REVERT: J 147 MET cc_start: 0.8260 (tpt) cc_final: 0.7899 (tpt) REVERT: J 163 MET cc_start: 0.8205 (mtp) cc_final: 0.7918 (mtp) REVERT: J 172 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7946 (mp) REVERT: K 35 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8133 (mp) REVERT: K 94 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8347 (tp) REVERT: K 111 MET cc_start: 0.8371 (mmm) cc_final: 0.8052 (mmm) REVERT: L 147 MET cc_start: 0.8025 (tpt) cc_final: 0.7718 (tpt) REVERT: L 172 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7863 (mp) REVERT: M 147 MET cc_start: 0.8332 (tpt) cc_final: 0.8066 (tpt) REVERT: M 172 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7821 (mp) REVERT: N 59 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7771 (mp) REVERT: N 147 MET cc_start: 0.8036 (tpt) cc_final: 0.7766 (tpt) outliers start: 97 outliers final: 46 residues processed: 406 average time/residue: 0.1187 time to fit residues: 77.9923 Evaluate side-chains 392 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 337 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 172 ILE Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 172 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 167 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 0.8980 chunk 231 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 246 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 HIS C 4 HIS E 4 HIS E 178 GLN F 67 ASN G 4 HIS I 4 HIS J 4 HIS L 4 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123447 restraints weight = 26933.695| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.39 r_work: 0.3440 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20496 Z= 0.112 Angle : 0.469 8.640 27832 Z= 0.232 Chirality : 0.040 0.164 3066 Planarity : 0.003 0.026 3598 Dihedral : 4.012 19.542 2786 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.78 % Allowed : 14.81 % Favored : 81.41 % 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 are not related in a simple way. whole: 1.61 (0.17), residues: 2534 helix: 2.72 (0.15), residues: 1204 sheet: -0.21 (0.19), residues: 616 loop : -0.62 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 3 TYR 0.022 0.001 TYR A 125 PHE 0.010 0.001 PHE K 8 TRP 0.007 0.001 TRP E 179 HIS 0.007 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00261 (20496) covalent geometry : angle 0.46874 (27832) hydrogen bonds : bond 0.02861 ( 1137) hydrogen bonds : angle 3.94146 ( 3402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 363 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8427 (t80) cc_final: 0.8210 (t80) REVERT: A 163 MET cc_start: 0.8170 (mmm) cc_final: 0.7360 (mmm) REVERT: B 30 GLN cc_start: 0.7935 (mp10) cc_final: 0.7372 (mp10) REVERT: B 74 MET cc_start: 0.7796 (mmm) cc_final: 0.7494 (mmm) REVERT: B 163 MET cc_start: 0.8267 (mtp) cc_final: 0.8001 (mmm) REVERT: C 16 THR cc_start: 0.8600 (m) cc_final: 0.8384 (p) REVERT: C 80 LEU cc_start: 0.8023 (mt) cc_final: 0.7645 (mp) REVERT: C 147 MET cc_start: 0.8066 (tpt) cc_final: 0.7850 (tpt) REVERT: D 172 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7570 (mp) REVERT: E 6 ILE cc_start: 0.7945 (mt) cc_final: 0.7713 (mt) REVERT: E 94 LEU cc_start: 0.8541 (tt) cc_final: 0.8320 (tp) REVERT: E 147 MET cc_start: 0.8054 (tpt) cc_final: 0.7738 (mmm) REVERT: E 170 MET cc_start: 0.8790 (mmp) cc_final: 0.8352 (tpp) REVERT: F 6 ILE cc_start: 0.7915 (mt) cc_final: 0.7694 (mt) REVERT: F 16 THR cc_start: 0.8496 (m) cc_final: 0.8258 (p) REVERT: F 74 MET cc_start: 0.8332 (mmm) cc_final: 0.7825 (mmm) REVERT: F 147 MET cc_start: 0.8092 (tpt) cc_final: 0.7775 (mmm) REVERT: G 147 MET cc_start: 0.8065 (tpt) cc_final: 0.7794 (tpt) REVERT: H 3 ARG cc_start: 0.8247 (ptm160) cc_final: 0.8043 (ttm-80) REVERT: H 9 THR cc_start: 0.8347 (m) cc_final: 0.8088 (p) REVERT: H 23 THR cc_start: 0.7898 (m) cc_final: 0.7662 (p) REVERT: H 65 THR cc_start: 0.7762 (p) cc_final: 0.7492 (p) REVERT: H 74 MET cc_start: 0.7936 (mmm) cc_final: 0.7299 (mmm) REVERT: H 111 MET cc_start: 0.8361 (mmm) cc_final: 0.7913 (mmm) REVERT: H 147 MET cc_start: 0.7879 (tpt) cc_final: 0.7561 (tpt) REVERT: I 16 THR cc_start: 0.8462 (m) cc_final: 0.8208 (p) REVERT: I 65 THR cc_start: 0.7804 (p) cc_final: 0.7443 (p) REVERT: J 35 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8000 (mt) REVERT: J 147 MET cc_start: 0.8188 (tpt) cc_final: 0.7831 (tpt) REVERT: J 163 MET cc_start: 0.8108 (mtp) cc_final: 0.7303 (mmm) REVERT: K 35 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8056 (mp) REVERT: K 94 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8306 (tp) REVERT: L 74 MET cc_start: 0.7944 (mmm) cc_final: 0.7453 (mmm) REVERT: L 147 MET cc_start: 0.7878 (tpt) cc_final: 0.7597 (tpt) REVERT: L 172 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7740 (mp) REVERT: M 35 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7843 (mp) REVERT: M 59 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7570 (mp) REVERT: M 147 MET cc_start: 0.8240 (tpt) cc_final: 0.7995 (tpt) REVERT: M 172 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7816 (mp) REVERT: N 30 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6804 (mp10) REVERT: N 59 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7631 (mp) REVERT: N 147 MET cc_start: 0.7941 (tpt) cc_final: 0.7679 (tpt) outliers start: 80 outliers final: 41 residues processed: 419 average time/residue: 0.1194 time to fit residues: 80.8791 Evaluate side-chains 414 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 363 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 172 ILE Chi-restraints excluded: chain N residue 30 GLN Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 167 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 157 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 145 optimal weight: 0.0050 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS B 4 HIS C 4 HIS C 96 HIS C 99 HIS C 156 GLN D 4 HIS E 4 HIS F 67 ASN H 4 HIS I 4 HIS ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 HIS L 4 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121216 restraints weight = 26885.415| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.37 r_work: 0.3421 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20496 Z= 0.191 Angle : 0.519 8.177 27832 Z= 0.259 Chirality : 0.042 0.220 3066 Planarity : 0.003 0.026 3598 Dihedral : 4.177 23.753 2786 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.93 % Allowed : 14.90 % Favored : 81.17 % 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 are not related in a simple way. whole: 1.46 (0.17), residues: 2534 helix: 2.66 (0.15), residues: 1204 sheet: -0.43 (0.19), residues: 616 loop : -0.65 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 3 TYR 0.028 0.002 TYR A 125 PHE 0.009 0.001 PHE C 93 TRP 0.005 0.001 TRP F 179 HIS 0.009 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00444 (20496) covalent geometry : angle 0.51851 (27832) hydrogen bonds : bond 0.03446 ( 1137) hydrogen bonds : angle 4.05790 ( 3402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 335 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.8203 (mmm) cc_final: 0.7262 (mmm) REVERT: B 163 MET cc_start: 0.8307 (mtp) cc_final: 0.7967 (mmm) REVERT: C 16 THR cc_start: 0.8620 (m) cc_final: 0.8368 (p) REVERT: C 147 MET cc_start: 0.8146 (tpt) cc_final: 0.7920 (tpt) REVERT: D 92 LYS cc_start: 0.8941 (pttt) cc_final: 0.8579 (pttm) REVERT: D 172 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7588 (mp) REVERT: E 6 ILE cc_start: 0.8029 (mt) cc_final: 0.7807 (mt) REVERT: E 94 LEU cc_start: 0.8548 (tt) cc_final: 0.8321 (tp) REVERT: E 147 MET cc_start: 0.8102 (tpt) cc_final: 0.7794 (mmm) REVERT: E 170 MET cc_start: 0.8787 (mmp) cc_final: 0.8338 (tpp) REVERT: F 6 ILE cc_start: 0.7988 (mt) cc_final: 0.7776 (mt) REVERT: F 16 THR cc_start: 0.8506 (m) cc_final: 0.8253 (p) REVERT: F 147 MET cc_start: 0.8144 (tpt) cc_final: 0.7820 (mmm) REVERT: G 65 THR cc_start: 0.7668 (p) cc_final: 0.7342 (p) REVERT: G 147 MET cc_start: 0.8140 (tpt) cc_final: 0.7868 (tpt) REVERT: H 3 ARG cc_start: 0.8287 (ptm160) cc_final: 0.8069 (ttm-80) REVERT: H 59 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7775 (mp) REVERT: H 111 MET cc_start: 0.8356 (mmm) cc_final: 0.7903 (mmm) REVERT: H 147 MET cc_start: 0.7967 (tpt) cc_final: 0.7652 (tpt) REVERT: H 172 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7520 (mp) REVERT: I 16 THR cc_start: 0.8496 (m) cc_final: 0.8219 (p) REVERT: I 65 THR cc_start: 0.7870 (p) cc_final: 0.7576 (p) REVERT: J 35 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8051 (mt) REVERT: J 147 MET cc_start: 0.8205 (tpt) cc_final: 0.7884 (tpt) REVERT: J 172 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (mp) REVERT: K 35 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8179 (mp) REVERT: K 94 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8327 (tp) REVERT: L 30 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: L 147 MET cc_start: 0.8014 (tpt) cc_final: 0.7715 (tpt) REVERT: L 172 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7803 (mp) REVERT: M 35 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7823 (mp) REVERT: M 59 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7735 (mp) REVERT: M 147 MET cc_start: 0.8270 (tpt) cc_final: 0.8027 (tpt) REVERT: M 172 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7857 (mp) REVERT: N 59 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7763 (mp) REVERT: N 147 MET cc_start: 0.7993 (tpt) cc_final: 0.7729 (tpt) outliers start: 83 outliers final: 47 residues processed: 387 average time/residue: 0.1245 time to fit residues: 76.9669 Evaluate side-chains 393 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 333 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 96 HIS Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 172 ILE Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 172 ILE Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 167 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 66 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS B 4 HIS C 4 HIS C 96 HIS D 4 HIS E 4 HIS F 67 ASN H 4 HIS I 4 HIS ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 HIS ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121886 restraints weight = 26798.358| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.36 r_work: 0.3428 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20496 Z= 0.159 Angle : 0.508 8.221 27832 Z= 0.251 Chirality : 0.041 0.219 3066 Planarity : 0.003 0.027 3598 Dihedral : 4.158 23.046 2786 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.78 % Allowed : 15.18 % Favored : 81.03 % 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 are not related in a simple way. whole: 1.48 (0.17), residues: 2534 helix: 2.65 (0.15), residues: 1204 sheet: -0.41 (0.19), residues: 616 loop : -0.62 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 3 TYR 0.027 0.002 TYR A 125 PHE 0.010 0.001 PHE C 95 TRP 0.006 0.001 TRP F 179 HIS 0.008 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00372 (20496) covalent geometry : angle 0.50829 (27832) hydrogen bonds : bond 0.03221 ( 1137) hydrogen bonds : angle 4.01805 ( 3402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 342 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8916 (pttt) cc_final: 0.8677 (pttm) REVERT: A 163 MET cc_start: 0.8238 (mmm) cc_final: 0.7324 (mmm) REVERT: B 74 MET cc_start: 0.7843 (mmm) cc_final: 0.7554 (mmm) REVERT: B 163 MET cc_start: 0.8273 (mtp) cc_final: 0.7976 (mmm) REVERT: C 16 THR cc_start: 0.8599 (m) cc_final: 0.8365 (p) REVERT: C 74 MET cc_start: 0.7792 (mmm) cc_final: 0.7276 (mmm) REVERT: C 147 MET cc_start: 0.8144 (tpt) cc_final: 0.7922 (tpt) REVERT: D 92 LYS cc_start: 0.8916 (pttt) cc_final: 0.8545 (pttm) REVERT: D 172 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7596 (mp) REVERT: E 6 ILE cc_start: 0.7948 (mt) cc_final: 0.7719 (mt) REVERT: E 94 LEU cc_start: 0.8532 (tt) cc_final: 0.8312 (tp) REVERT: E 147 MET cc_start: 0.8061 (tpt) cc_final: 0.7757 (mmm) REVERT: E 170 MET cc_start: 0.8773 (mmp) cc_final: 0.8320 (tpp) REVERT: F 6 ILE cc_start: 0.7963 (mt) cc_final: 0.7744 (mt) REVERT: F 16 THR cc_start: 0.8510 (m) cc_final: 0.8266 (p) REVERT: F 147 MET cc_start: 0.8119 (tpt) cc_final: 0.7793 (tpt) REVERT: G 65 THR cc_start: 0.7650 (p) cc_final: 0.7328 (p) REVERT: G 147 MET cc_start: 0.8097 (tpt) cc_final: 0.7831 (tpt) REVERT: H 3 ARG cc_start: 0.8254 (ptm160) cc_final: 0.8052 (ttm-80) REVERT: H 111 MET cc_start: 0.8357 (mmm) cc_final: 0.7909 (mmm) REVERT: H 147 MET cc_start: 0.7946 (tpt) cc_final: 0.7638 (tpt) REVERT: H 172 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7498 (mp) REVERT: I 16 THR cc_start: 0.8487 (m) cc_final: 0.8230 (p) REVERT: J 35 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8024 (mt) REVERT: J 147 MET cc_start: 0.8211 (tpt) cc_final: 0.7891 (tpt) REVERT: J 163 MET cc_start: 0.8130 (mtp) cc_final: 0.7282 (mmm) REVERT: J 172 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7888 (mp) REVERT: K 35 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8193 (mp) REVERT: K 94 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8310 (tp) REVERT: L 30 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: L 147 MET cc_start: 0.7987 (tpt) cc_final: 0.7697 (tpt) REVERT: L 172 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7767 (mp) REVERT: M 35 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7842 (mp) REVERT: M 59 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7690 (mp) REVERT: M 147 MET cc_start: 0.8252 (tpt) cc_final: 0.8015 (tpt) REVERT: M 172 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7837 (mp) REVERT: N 30 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6860 (mp10) REVERT: N 59 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7715 (mp) REVERT: N 147 MET cc_start: 0.7929 (tpt) cc_final: 0.7692 (tpt) outliers start: 80 outliers final: 50 residues processed: 394 average time/residue: 0.1233 time to fit residues: 77.8159 Evaluate side-chains 405 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 342 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 96 HIS Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 172 ILE Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 172 ILE Chi-restraints excluded: chain N residue 30 GLN Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 56 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 213 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 143 optimal weight: 0.0570 overall best weight: 0.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS B 4 HIS C 4 HIS C 96 HIS E 4 HIS F 67 ASN I 67 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 HIS ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123304 restraints weight = 26902.434| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.38 r_work: 0.3438 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20496 Z= 0.108 Angle : 0.489 10.578 27832 Z= 0.237 Chirality : 0.040 0.214 3066 Planarity : 0.003 0.027 3598 Dihedral : 4.037 21.873 2786 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.12 % Allowed : 15.61 % Favored : 81.27 % 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 are not related in a simple way. whole: 1.65 (0.17), residues: 2534 helix: 2.73 (0.15), residues: 1204 sheet: -0.10 (0.20), residues: 602 loop : -0.63 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 3 TYR 0.024 0.001 TYR A 125 PHE 0.021 0.001 PHE D 50 TRP 0.007 0.001 TRP F 179 HIS 0.007 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00253 (20496) covalent geometry : angle 0.48882 (27832) hydrogen bonds : bond 0.02818 ( 1137) hydrogen bonds : angle 3.91770 ( 3402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 352 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8803 (pttt) cc_final: 0.8536 (pttm) REVERT: A 163 MET cc_start: 0.8277 (mmm) cc_final: 0.7447 (mmm) REVERT: B 74 MET cc_start: 0.7687 (mmm) cc_final: 0.7482 (mmm) REVERT: B 163 MET cc_start: 0.8272 (mtp) cc_final: 0.7998 (mmm) REVERT: C 16 THR cc_start: 0.8623 (m) cc_final: 0.8387 (p) REVERT: C 74 MET cc_start: 0.7704 (mmm) cc_final: 0.7255 (mmm) REVERT: D 92 LYS cc_start: 0.8886 (pttt) cc_final: 0.8528 (pttm) REVERT: D 172 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7539 (mp) REVERT: E 6 ILE cc_start: 0.7885 (mt) cc_final: 0.7652 (mt) REVERT: E 94 LEU cc_start: 0.8534 (tt) cc_final: 0.8306 (tp) REVERT: E 147 MET cc_start: 0.8028 (tpt) cc_final: 0.7724 (mmm) REVERT: F 6 ILE cc_start: 0.7901 (mt) cc_final: 0.7679 (mt) REVERT: F 16 THR cc_start: 0.8485 (m) cc_final: 0.8242 (p) REVERT: F 147 MET cc_start: 0.8028 (tpt) cc_final: 0.7700 (tpt) REVERT: G 65 THR cc_start: 0.7621 (p) cc_final: 0.7289 (p) REVERT: G 147 MET cc_start: 0.7956 (tpt) cc_final: 0.7720 (tpt) REVERT: H 111 MET cc_start: 0.8350 (mmm) cc_final: 0.7932 (mmm) REVERT: H 147 MET cc_start: 0.7781 (tpt) cc_final: 0.7482 (tpt) REVERT: I 16 THR cc_start: 0.8531 (m) cc_final: 0.8281 (p) REVERT: J 35 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7911 (mt) REVERT: J 74 MET cc_start: 0.7826 (mmm) cc_final: 0.6969 (mmm) REVERT: J 147 MET cc_start: 0.8134 (tpt) cc_final: 0.7837 (tpt) REVERT: J 163 MET cc_start: 0.8070 (mtp) cc_final: 0.7234 (mmm) REVERT: K 35 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (mp) REVERT: K 94 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8360 (tp) REVERT: K 172 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7835 (mp) REVERT: L 30 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: L 147 MET cc_start: 0.7862 (tpt) cc_final: 0.7590 (mmm) REVERT: L 172 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7725 (mp) REVERT: M 35 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7863 (mp) REVERT: M 59 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7568 (mp) REVERT: M 147 MET cc_start: 0.8116 (tpt) cc_final: 0.7892 (tpt) REVERT: M 172 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7852 (mp) REVERT: N 147 MET cc_start: 0.7926 (tpt) cc_final: 0.7685 (tpt) outliers start: 66 outliers final: 44 residues processed: 395 average time/residue: 0.1181 time to fit residues: 75.3200 Evaluate side-chains 405 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 351 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 172 ILE Chi-restraints excluded: chain N residue 30 GLN Chi-restraints excluded: chain N residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS B 4 HIS C 4 HIS ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 HIS D 4 HIS E 4 HIS F 67 ASN F 96 HIS F 99 HIS I 4 HIS ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 HIS ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122719 restraints weight = 27089.248| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.38 r_work: 0.3429 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20496 Z= 0.127 Angle : 0.507 11.784 27832 Z= 0.245 Chirality : 0.041 0.220 3066 Planarity : 0.003 0.029 3598 Dihedral : 4.048 21.428 2786 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.55 % Allowed : 15.75 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.17), residues: 2534 helix: 2.73 (0.15), residues: 1204 sheet: -0.11 (0.20), residues: 602 loop : -0.61 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 3 TYR 0.027 0.001 TYR A 125 PHE 0.009 0.001 PHE F 50 TRP 0.006 0.000 TRP F 179 HIS 0.007 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00298 (20496) covalent geometry : angle 0.50705 (27832) hydrogen bonds : bond 0.02962 ( 1137) hydrogen bonds : angle 3.90985 ( 3402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.50 seconds wall clock time: 69 minutes 32.05 seconds (4172.05 seconds total)