Starting phenix.real_space_refine on Sat Oct 11 08:30:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjl_43288/10_2025/8vjl_43288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjl_43288/10_2025/8vjl_43288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vjl_43288/10_2025/8vjl_43288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjl_43288/10_2025/8vjl_43288.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjl_43288/10_2025/8vjl_43288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjl_43288/10_2025/8vjl_43288.cif" } resolution = 3.5 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= 0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 56 5.16 5 C 8846 2.51 5 N 2162 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13334 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'LMN': 1, 'PEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'LMN': 1, 'PEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.67, per 1000 atoms: 0.28 Number of scatterers: 13334 At special positions: 0 Unit cell: (135.16, 108.128, 89.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 2 15.00 O 2268 8.00 N 2162 7.00 C 8846 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: 1.33 Conformation dependent library (CDL) restraints added in 683.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 8 sheets defined 67.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.980A pdb=" N TRP A 18 " --> pdb=" O HIS A 14 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 54 removed outlier: 3.658A pdb=" N HIS A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.882A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.793A pdb=" N LEU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 130 removed outlier: 3.639A pdb=" N PHE A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 4.088A pdb=" N LEU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 178 Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.905A pdb=" N TRP A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.599A pdb=" N ALA A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.793A pdb=" N VAL A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 47 Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.554A pdb=" N ARG B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 removed outlier: 3.996A pdb=" N VAL B 63 " --> pdb=" O ASN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 94 removed outlier: 4.087A pdb=" N LEU B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 126 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 14 through 28 removed outlier: 3.732A pdb=" N TRP C 18 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 19 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 53 removed outlier: 3.965A pdb=" N HIS C 47 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.538A pdb=" N GLU C 83 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 removed outlier: 4.228A pdb=" N TRP C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.568A pdb=" N LEU C 117 " --> pdb=" O HIS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 148 Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.685A pdb=" N ASN C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 160 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 200 removed outlier: 3.625A pdb=" N TRP C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 4.081A pdb=" N ILE C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.621A pdb=" N VAL C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 241 " --> pdb=" O HIS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'D' and resid 35 through 47 removed outlier: 3.646A pdb=" N LYS D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 58 removed outlier: 3.642A pdb=" N ARG D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.842A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 94 removed outlier: 3.776A pdb=" N LEU D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.538A pdb=" N LYS D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 100' Processing helix chain 'D' and resid 102 through 126 removed outlier: 3.515A pdb=" N TYR D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 14 through 26 removed outlier: 3.980A pdb=" N TRP E 18 " --> pdb=" O HIS E 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 54 removed outlier: 3.645A pdb=" N HIS E 47 " --> pdb=" O HIS E 43 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 removed outlier: 3.883A pdb=" N ILE E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 93 through 107 removed outlier: 3.780A pdb=" N LEU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 130 removed outlier: 3.642A pdb=" N PHE E 115 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 116 " --> pdb=" O GLN E 112 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU E 117 " --> pdb=" O HIS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 removed outlier: 4.104A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 178 Processing helix chain 'E' and resid 181 through 200 removed outlier: 3.913A pdb=" N TRP E 185 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 234 through 240 removed outlier: 3.550A pdb=" N ALA E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 274 removed outlier: 3.785A pdb=" N VAL E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 47 Processing helix chain 'F' and resid 48 through 58 removed outlier: 3.557A pdb=" N ARG F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 70 removed outlier: 3.897A pdb=" N VAL F 63 " --> pdb=" O ASN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 94 removed outlier: 4.105A pdb=" N LEU F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 126 Processing helix chain 'G' and resid 2 through 9 Processing helix chain 'G' and resid 14 through 28 removed outlier: 3.732A pdb=" N TRP G 18 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 19 " --> pdb=" O PRO G 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 53 removed outlier: 3.966A pdb=" N HIS G 47 " --> pdb=" O HIS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.538A pdb=" N GLU G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 4.227A pdb=" N TRP G 96 " --> pdb=" O LEU G 92 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 107 " --> pdb=" O MET G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.572A pdb=" N LEU G 117 " --> pdb=" O HIS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 148 removed outlier: 3.573A pdb=" N LYS G 148 " --> pdb=" O LEU G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 removed outlier: 3.708A pdb=" N ASN G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 160 " --> pdb=" O HIS G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 200 removed outlier: 3.610A pdb=" N TRP G 185 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL G 186 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 4.086A pdb=" N ILE G 205 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 removed outlier: 3.619A pdb=" N VAL G 238 " --> pdb=" O LYS G 234 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU G 241 " --> pdb=" O HIS G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 273 Processing helix chain 'G' and resid 280 through 286 Processing helix chain 'H' and resid 35 through 47 removed outlier: 3.611A pdb=" N LYS H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 58 removed outlier: 3.654A pdb=" N ARG H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 70 removed outlier: 4.410A pdb=" N VAL H 63 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 94 removed outlier: 3.621A pdb=" N LEU H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.545A pdb=" N GLY H 100 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 126 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 64 removed outlier: 4.070A pdb=" N ARG A 60 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY A 68 " --> pdb=" O TYR B 22 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LYS B 24 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 70 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 6.062A pdb=" N LEU A 227 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU A 253 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 229 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 260 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS A 254 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 63 through 64 removed outlier: 7.375A pdb=" N GLY C 68 " --> pdb=" O TYR D 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 227 through 228 removed outlier: 7.361A pdb=" N LEU C 227 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLU C 253 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE C 250 " --> pdb=" O GLN C 261 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN C 261 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE C 252 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 257 " --> pdb=" O LYS C 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 12 through 13 removed outlier: 4.152A pdb=" N ARG E 60 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY E 68 " --> pdb=" O TYR F 22 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS F 24 " --> pdb=" O GLY E 68 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL E 70 " --> pdb=" O LYS F 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 227 through 230 removed outlier: 6.056A pdb=" N LEU E 227 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU E 253 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL E 229 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER E 260 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS E 254 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS E 258 " --> pdb=" O LYS E 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 63 through 64 removed outlier: 7.363A pdb=" N GLY G 68 " --> pdb=" O TYR H 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 227 through 228 removed outlier: 7.365A pdb=" N LEU G 227 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLU G 253 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE G 250 " --> pdb=" O GLN G 261 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN G 261 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE G 252 " --> pdb=" O LEU G 259 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN G 257 " --> pdb=" O LYS G 254 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2012 1.31 - 1.43: 3620 1.43 - 1.56: 7896 1.56 - 1.68: 64 1.68 - 1.81: 88 Bond restraints: 13680 Sorted by residual: bond pdb=" C1 LMN E 401 " pdb=" O5 LMN E 401 " ideal model delta sigma weight residual 1.403 1.537 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C1 LMN A 401 " pdb=" O5 LMN A 401 " ideal model delta sigma weight residual 1.403 1.537 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C1 LMN C 401 " pdb=" O5 LMN C 401 " ideal model delta sigma weight residual 1.403 1.537 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C1 LMN G 401 " pdb=" O5 LMN G 401 " ideal model delta sigma weight residual 1.403 1.537 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" CBS LMN E 401 " pdb=" CCM LMN E 401 " ideal model delta sigma weight residual 1.529 1.630 -0.101 2.00e-02 2.50e+03 2.55e+01 ... (remaining 13675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 18176 2.98 - 5.97: 310 5.97 - 8.95: 20 8.95 - 11.94: 10 11.94 - 14.92: 2 Bond angle restraints: 18518 Sorted by residual: angle pdb=" O3P PEF A 402 " pdb=" P PEF A 402 " pdb=" O4P PEF A 402 " ideal model delta sigma weight residual 93.96 108.88 -14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O3P PEF E 402 " pdb=" P PEF E 402 " pdb=" O4P PEF E 402 " ideal model delta sigma weight residual 93.96 108.86 -14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1P PEF A 402 " pdb=" P PEF A 402 " pdb=" O2P PEF A 402 " ideal model delta sigma weight residual 119.53 109.21 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" O1P PEF E 402 " pdb=" P PEF E 402 " pdb=" O2P PEF E 402 " ideal model delta sigma weight residual 119.53 109.28 10.25 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CCQ LMN A 401 " pdb=" OCB LMN A 401 " pdb=" CCS LMN A 401 " ideal model delta sigma weight residual 119.65 109.45 10.20 3.00e+00 1.11e-01 1.16e+01 ... (remaining 18513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 7582 25.01 - 50.02: 602 50.02 - 75.04: 123 75.04 - 100.05: 35 100.05 - 125.06: 68 Dihedral angle restraints: 8410 sinusoidal: 3682 harmonic: 4728 Sorted by residual: dihedral pdb=" O2 LMN C 401 " pdb=" C2 LMN C 401 " pdb=" C3 LMN C 401 " pdb=" O3 LMN C 401 " ideal model delta sinusoidal sigma weight residual 295.11 170.05 125.06 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" O2 LMN G 401 " pdb=" C2 LMN G 401 " pdb=" C3 LMN G 401 " pdb=" O3 LMN G 401 " ideal model delta sinusoidal sigma weight residual 295.11 170.08 125.03 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C1 LMN C 401 " pdb=" C2 LMN C 401 " pdb=" C3 LMN C 401 " pdb=" O3 LMN C 401 " ideal model delta sinusoidal sigma weight residual 174.26 50.75 123.51 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 8407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1609 0.043 - 0.085: 424 0.085 - 0.128: 88 0.128 - 0.170: 13 0.170 - 0.213: 8 Chirality restraints: 2142 Sorted by residual: chirality pdb=" C1 LMN C 401 " pdb=" C2 LMN C 401 " pdb=" O1 LMN C 401 " pdb=" O5 LMN C 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.50 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C1 LMN G 401 " pdb=" C2 LMN G 401 " pdb=" O1 LMN G 401 " pdb=" O5 LMN G 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.50 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C1 LMN E 401 " pdb=" C2 LMN E 401 " pdb=" O1 LMN E 401 " pdb=" O5 LMN E 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2139 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 178 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 179 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 178 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO G 179 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 179 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 179 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 64 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 65 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 65 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 65 " 0.019 5.00e-02 4.00e+02 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1742 2.75 - 3.29: 12845 3.29 - 3.83: 20777 3.83 - 4.36: 22337 4.36 - 4.90: 40334 Nonbonded interactions: 98035 Sorted by model distance: nonbonded pdb=" OG SER D 33 " pdb=" OE1 GLU D 36 " model vdw 2.215 3.040 nonbonded pdb=" ND1 HIS A 94 " pdb=" OD1 ASN A 122 " model vdw 2.245 3.120 nonbonded pdb=" ND1 HIS E 94 " pdb=" OD1 ASN E 122 " model vdw 2.245 3.120 nonbonded pdb=" OD1 ASP E 233 " pdb=" N LYS E 234 " model vdw 2.255 3.120 nonbonded pdb=" O LYS B 90 " pdb=" OG SER B 94 " model vdw 2.265 3.040 ... (remaining 98030 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' and resid 1 through 401) selection = chain 'C' selection = (chain 'E' and resid 1 through 401) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 13680 Z= 0.390 Angle : 0.793 14.922 18518 Z= 0.339 Chirality : 0.041 0.213 2142 Planarity : 0.004 0.040 2220 Dihedral : 22.663 125.060 5338 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.81 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.22), residues: 1600 helix: 1.60 (0.17), residues: 1044 sheet: 1.75 (0.62), residues: 48 loop : -2.13 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 208 TYR 0.012 0.001 TYR D 95 PHE 0.011 0.001 PHE D 11 TRP 0.017 0.001 TRP C 96 HIS 0.011 0.001 HIS H 65 Details of bonding type rmsd covalent geometry : bond 0.00789 (13680) covalent geometry : angle 0.79349 (18518) hydrogen bonds : bond 0.14736 ( 748) hydrogen bonds : angle 4.34974 ( 2220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.583 Fit side-chains REVERT: E 233 ASP cc_start: 0.7214 (t0) cc_final: 0.6976 (t0) REVERT: G 274 ASP cc_start: 0.7415 (m-30) cc_final: 0.7202 (m-30) REVERT: H 14 LYS cc_start: 0.7854 (tptp) cc_final: 0.7602 (pttp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1242 time to fit residues: 42.4518 Evaluate side-chains 199 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 HIS A 265 ASN B 118 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN F 118 HIS G 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.191619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141336 restraints weight = 17967.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140604 restraints weight = 10611.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141846 restraints weight = 8829.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142342 restraints weight = 7495.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142352 restraints weight = 7189.240| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13680 Z= 0.163 Angle : 0.677 9.705 18518 Z= 0.320 Chirality : 0.045 0.270 2142 Planarity : 0.004 0.040 2220 Dihedral : 18.291 94.394 2306 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.31 % Favored : 92.19 % Rotamer: Outliers : 1.03 % Allowed : 9.07 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.22), residues: 1600 helix: 1.44 (0.16), residues: 1064 sheet: 1.56 (0.62), residues: 48 loop : -2.27 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.007 0.001 TYR D 22 PHE 0.014 0.001 PHE C 62 TRP 0.015 0.001 TRP C 96 HIS 0.005 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00383 (13680) covalent geometry : angle 0.67731 (18518) hydrogen bonds : bond 0.05524 ( 748) hydrogen bonds : angle 3.72374 ( 2220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6648 (m-10) cc_final: 0.6411 (m-10) REVERT: A 281 MET cc_start: 0.7119 (ppp) cc_final: 0.5224 (ptp) REVERT: B 117 MET cc_start: 0.7878 (ttt) cc_final: 0.7662 (ttm) REVERT: C 274 ASP cc_start: 0.6970 (m-30) cc_final: 0.6231 (m-30) REVERT: D 117 MET cc_start: 0.7608 (tpp) cc_final: 0.7232 (mtp) REVERT: E 215 TYR cc_start: 0.6612 (m-10) cc_final: 0.6388 (m-10) REVERT: E 281 MET cc_start: 0.7212 (ppp) cc_final: 0.5362 (ptp) REVERT: F 106 TYR cc_start: 0.7415 (t80) cc_final: 0.7199 (t80) REVERT: G 274 ASP cc_start: 0.7177 (m-30) cc_final: 0.6773 (m-30) REVERT: H 14 LYS cc_start: 0.7802 (tptp) cc_final: 0.7574 (pttp) REVERT: H 106 TYR cc_start: 0.7158 (t80) cc_final: 0.6881 (t80) outliers start: 14 outliers final: 10 residues processed: 203 average time/residue: 0.1292 time to fit residues: 37.3016 Evaluate side-chains 195 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 172 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 HIS B 118 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN F 118 HIS ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.192980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143859 restraints weight = 18268.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142833 restraints weight = 11539.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142771 restraints weight = 8766.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143688 restraints weight = 8833.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143726 restraints weight = 7923.777| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13680 Z= 0.132 Angle : 0.636 12.946 18518 Z= 0.298 Chirality : 0.042 0.278 2142 Planarity : 0.004 0.037 2220 Dihedral : 14.659 87.116 2306 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.69 % Favored : 92.81 % Rotamer: Outliers : 1.11 % Allowed : 11.36 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.22), residues: 1600 helix: 1.49 (0.16), residues: 1064 sheet: 1.59 (0.63), residues: 48 loop : -2.29 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 78 TYR 0.006 0.001 TYR H 22 PHE 0.012 0.001 PHE G 99 TRP 0.015 0.001 TRP C 96 HIS 0.008 0.001 HIS H 65 Details of bonding type rmsd covalent geometry : bond 0.00301 (13680) covalent geometry : angle 0.63584 (18518) hydrogen bonds : bond 0.04919 ( 748) hydrogen bonds : angle 3.61930 ( 2220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7077 (ppp) cc_final: 0.5229 (ptp) REVERT: B 68 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7506 (ttpt) REVERT: C 274 ASP cc_start: 0.6994 (m-30) cc_final: 0.6218 (m-30) REVERT: C 281 MET cc_start: 0.6793 (pmm) cc_final: 0.6414 (pmm) REVERT: D 117 MET cc_start: 0.7648 (tpp) cc_final: 0.7444 (tpt) REVERT: E 281 MET cc_start: 0.7077 (ppp) cc_final: 0.5257 (ptp) REVERT: F 36 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: G 274 ASP cc_start: 0.7175 (m-30) cc_final: 0.6777 (m-30) REVERT: G 281 MET cc_start: 0.6827 (pmm) cc_final: 0.6443 (pmm) REVERT: H 14 LYS cc_start: 0.7812 (tptp) cc_final: 0.7565 (pttp) REVERT: H 106 TYR cc_start: 0.7297 (t80) cc_final: 0.7017 (t80) outliers start: 15 outliers final: 10 residues processed: 216 average time/residue: 0.1302 time to fit residues: 39.7694 Evaluate side-chains 199 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 172 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 126 optimal weight: 0.0270 chunk 60 optimal weight: 9.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN F 118 HIS G 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.196470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148314 restraints weight = 17996.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146979 restraints weight = 11230.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147291 restraints weight = 9205.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148299 restraints weight = 8306.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148327 restraints weight = 7488.984| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13680 Z= 0.106 Angle : 0.561 11.555 18518 Z= 0.270 Chirality : 0.040 0.351 2142 Planarity : 0.004 0.034 2220 Dihedral : 11.490 89.949 2306 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.81 % Favored : 92.69 % Rotamer: Outliers : 1.33 % Allowed : 13.94 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.22), residues: 1600 helix: 1.66 (0.16), residues: 1064 sheet: 0.81 (0.65), residues: 56 loop : -2.26 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 61 TYR 0.007 0.001 TYR F 106 PHE 0.008 0.001 PHE D 11 TRP 0.014 0.001 TRP C 96 HIS 0.004 0.001 HIS H 65 Details of bonding type rmsd covalent geometry : bond 0.00226 (13680) covalent geometry : angle 0.56139 (18518) hydrogen bonds : bond 0.03888 ( 748) hydrogen bonds : angle 3.44136 ( 2220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7088 (ppp) cc_final: 0.5255 (ptp) REVERT: B 36 GLU cc_start: 0.8711 (pm20) cc_final: 0.8180 (pm20) REVERT: B 68 LYS cc_start: 0.7595 (ttpp) cc_final: 0.7388 (ttpt) REVERT: B 106 TYR cc_start: 0.7400 (t80) cc_final: 0.7161 (t80) REVERT: C 274 ASP cc_start: 0.6974 (m-30) cc_final: 0.6692 (m-30) REVERT: C 281 MET cc_start: 0.6881 (pmm) cc_final: 0.6577 (pmm) REVERT: D 117 MET cc_start: 0.7644 (tpp) cc_final: 0.7407 (tpp) REVERT: E 281 MET cc_start: 0.6959 (ppp) cc_final: 0.5266 (ptp) REVERT: F 36 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: G 274 ASP cc_start: 0.6933 (m-30) cc_final: 0.6538 (m-30) REVERT: G 281 MET cc_start: 0.6952 (pmm) cc_final: 0.6626 (pmm) REVERT: H 14 LYS cc_start: 0.7823 (tptp) cc_final: 0.7517 (pttp) REVERT: H 106 TYR cc_start: 0.7398 (t80) cc_final: 0.7011 (t80) outliers start: 18 outliers final: 12 residues processed: 215 average time/residue: 0.1292 time to fit residues: 39.4415 Evaluate side-chains 200 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN E 265 ASN F 118 HIS ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.190992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142417 restraints weight = 18139.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140466 restraints weight = 11817.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140100 restraints weight = 10345.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141200 restraints weight = 9224.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141096 restraints weight = 8139.540| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13680 Z= 0.165 Angle : 0.640 13.295 18518 Z= 0.308 Chirality : 0.043 0.371 2142 Planarity : 0.004 0.036 2220 Dihedral : 11.025 88.688 2306 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.62 % Favored : 92.88 % Rotamer: Outliers : 2.06 % Allowed : 15.27 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.22), residues: 1600 helix: 1.46 (0.16), residues: 1060 sheet: 0.68 (0.64), residues: 56 loop : -2.18 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 60 TYR 0.012 0.001 TYR E 271 PHE 0.015 0.001 PHE C 62 TRP 0.012 0.001 TRP E 96 HIS 0.006 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00399 (13680) covalent geometry : angle 0.63969 (18518) hydrogen bonds : bond 0.05368 ( 748) hydrogen bonds : angle 3.59442 ( 2220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7444 (tt) REVERT: A 271 TYR cc_start: 0.8242 (t80) cc_final: 0.7940 (t80) REVERT: A 281 MET cc_start: 0.7082 (ppp) cc_final: 0.5217 (ptp) REVERT: B 36 GLU cc_start: 0.8542 (pm20) cc_final: 0.7792 (pm20) REVERT: B 37 GLU cc_start: 0.8453 (pt0) cc_final: 0.8252 (pt0) REVERT: B 39 LYS cc_start: 0.8398 (pttp) cc_final: 0.8078 (tptp) REVERT: B 68 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7436 (ttmt) REVERT: B 106 TYR cc_start: 0.7345 (t80) cc_final: 0.7117 (t80) REVERT: C 274 ASP cc_start: 0.6884 (m-30) cc_final: 0.6076 (m-30) REVERT: C 281 MET cc_start: 0.7000 (pmm) cc_final: 0.6488 (pmm) REVERT: C 282 GLU cc_start: 0.5887 (mp0) cc_final: 0.5658 (mp0) REVERT: D 90 LYS cc_start: 0.5731 (mttp) cc_final: 0.5506 (mttm) REVERT: D 117 MET cc_start: 0.7687 (tpp) cc_final: 0.7427 (tpp) REVERT: E 164 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7439 (tt) REVERT: E 271 TYR cc_start: 0.8269 (t80) cc_final: 0.7892 (t80) REVERT: E 281 MET cc_start: 0.7028 (ppp) cc_final: 0.5172 (ptp) REVERT: F 39 LYS cc_start: 0.8291 (pttp) cc_final: 0.8016 (mmmt) REVERT: G 274 ASP cc_start: 0.6845 (m-30) cc_final: 0.6473 (m-30) REVERT: G 281 MET cc_start: 0.7092 (pmm) cc_final: 0.6527 (pmm) REVERT: G 282 GLU cc_start: 0.5873 (mp0) cc_final: 0.5649 (mp0) REVERT: H 14 LYS cc_start: 0.7856 (tptp) cc_final: 0.7587 (ptmm) REVERT: H 106 TYR cc_start: 0.7517 (t80) cc_final: 0.7178 (t80) outliers start: 28 outliers final: 19 residues processed: 212 average time/residue: 0.1284 time to fit residues: 38.9030 Evaluate side-chains 204 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 41 optimal weight: 2.9990 chunk 119 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN F 65 HIS F 118 HIS G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.195814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.147082 restraints weight = 18004.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146494 restraints weight = 10867.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146445 restraints weight = 8488.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146998 restraints weight = 8158.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147544 restraints weight = 7406.784| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13680 Z= 0.106 Angle : 0.549 13.843 18518 Z= 0.267 Chirality : 0.039 0.317 2142 Planarity : 0.004 0.034 2220 Dihedral : 10.021 89.665 2306 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.44 % Favored : 93.06 % Rotamer: Outliers : 1.55 % Allowed : 17.04 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.22), residues: 1600 helix: 1.67 (0.16), residues: 1064 sheet: 0.77 (0.66), residues: 56 loop : -2.24 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.011 0.001 TYR E 271 PHE 0.007 0.001 PHE H 70 TRP 0.017 0.001 TRP G 96 HIS 0.004 0.001 HIS H 65 Details of bonding type rmsd covalent geometry : bond 0.00233 (13680) covalent geometry : angle 0.54872 (18518) hydrogen bonds : bond 0.03894 ( 748) hydrogen bonds : angle 3.41358 ( 2220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 TYR cc_start: 0.8291 (t80) cc_final: 0.8069 (t80) REVERT: A 281 MET cc_start: 0.6946 (ppp) cc_final: 0.5132 (ptp) REVERT: B 36 GLU cc_start: 0.8515 (pm20) cc_final: 0.7751 (pm20) REVERT: B 39 LYS cc_start: 0.8303 (pttp) cc_final: 0.8071 (tptp) REVERT: B 68 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7379 (ttmt) REVERT: B 106 TYR cc_start: 0.7466 (t80) cc_final: 0.7224 (t80) REVERT: C 274 ASP cc_start: 0.7065 (m-30) cc_final: 0.6292 (m-30) REVERT: C 281 MET cc_start: 0.6969 (pmm) cc_final: 0.6479 (pmm) REVERT: E 281 MET cc_start: 0.6866 (ppp) cc_final: 0.4978 (ptp) REVERT: F 36 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: G 274 ASP cc_start: 0.6980 (m-30) cc_final: 0.6607 (m-30) REVERT: G 281 MET cc_start: 0.6929 (pmm) cc_final: 0.6315 (pmm) REVERT: G 282 GLU cc_start: 0.5830 (mp0) cc_final: 0.5581 (mp0) REVERT: H 14 LYS cc_start: 0.7850 (tptp) cc_final: 0.7520 (pttp) REVERT: H 106 TYR cc_start: 0.7404 (t80) cc_final: 0.7063 (t80) outliers start: 21 outliers final: 18 residues processed: 207 average time/residue: 0.1256 time to fit residues: 37.4178 Evaluate side-chains 194 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 22 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN F 65 HIS F 118 HIS G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.194443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146307 restraints weight = 18113.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144527 restraints weight = 10509.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144705 restraints weight = 8790.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145366 restraints weight = 8231.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145534 restraints weight = 7440.300| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13680 Z= 0.117 Angle : 0.564 14.234 18518 Z= 0.273 Chirality : 0.039 0.282 2142 Planarity : 0.004 0.034 2220 Dihedral : 9.792 86.116 2306 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.25 % Favored : 93.25 % Rotamer: Outliers : 1.84 % Allowed : 17.33 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.22), residues: 1600 helix: 1.67 (0.16), residues: 1060 sheet: 0.71 (0.66), residues: 56 loop : -2.13 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 78 TYR 0.014 0.001 TYR E 271 PHE 0.016 0.001 PHE C 99 TRP 0.012 0.001 TRP C 96 HIS 0.006 0.001 HIS F 65 Details of bonding type rmsd covalent geometry : bond 0.00266 (13680) covalent geometry : angle 0.56370 (18518) hydrogen bonds : bond 0.04213 ( 748) hydrogen bonds : angle 3.45000 ( 2220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7262 (tt) REVERT: A 271 TYR cc_start: 0.8274 (t80) cc_final: 0.8058 (t80) REVERT: A 281 MET cc_start: 0.6978 (ppp) cc_final: 0.5139 (ptp) REVERT: B 36 GLU cc_start: 0.8581 (pm20) cc_final: 0.7915 (pm20) REVERT: B 39 LYS cc_start: 0.8328 (pttp) cc_final: 0.8099 (tptp) REVERT: B 106 TYR cc_start: 0.7453 (t80) cc_final: 0.7227 (t80) REVERT: C 274 ASP cc_start: 0.7058 (m-30) cc_final: 0.6297 (m-30) REVERT: C 281 MET cc_start: 0.6947 (pmm) cc_final: 0.6298 (pmm) REVERT: C 282 GLU cc_start: 0.5831 (mp0) cc_final: 0.5596 (mp0) REVERT: D 117 MET cc_start: 0.7499 (tpp) cc_final: 0.7260 (mtp) REVERT: E 164 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7259 (tt) REVERT: E 281 MET cc_start: 0.6849 (ppp) cc_final: 0.4992 (ptp) REVERT: G 274 ASP cc_start: 0.6940 (m-30) cc_final: 0.6603 (m-30) REVERT: G 281 MET cc_start: 0.6944 (pmm) cc_final: 0.6389 (pmm) REVERT: H 14 LYS cc_start: 0.7823 (tptp) cc_final: 0.7515 (pttp) REVERT: H 106 TYR cc_start: 0.7501 (t80) cc_final: 0.7153 (t80) outliers start: 25 outliers final: 19 residues processed: 202 average time/residue: 0.1277 time to fit residues: 36.7148 Evaluate side-chains 200 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS B 118 HIS C 77 ASN F 118 HIS G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.194847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146317 restraints weight = 17940.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145406 restraints weight = 10700.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144966 restraints weight = 8733.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145821 restraints weight = 8796.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145897 restraints weight = 7850.836| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13680 Z= 0.113 Angle : 0.557 14.561 18518 Z= 0.274 Chirality : 0.039 0.225 2142 Planarity : 0.004 0.034 2220 Dihedral : 9.538 81.980 2306 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.62 % Favored : 92.88 % Rotamer: Outliers : 2.51 % Allowed : 17.04 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.22), residues: 1600 helix: 1.70 (0.16), residues: 1060 sheet: 0.64 (0.66), residues: 56 loop : -2.10 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 61 TYR 0.014 0.001 TYR E 271 PHE 0.009 0.001 PHE G 62 TRP 0.013 0.001 TRP G 96 HIS 0.004 0.001 HIS H 65 Details of bonding type rmsd covalent geometry : bond 0.00255 (13680) covalent geometry : angle 0.55712 (18518) hydrogen bonds : bond 0.04108 ( 748) hydrogen bonds : angle 3.44702 ( 2220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7183 (tt) REVERT: A 237 HIS cc_start: 0.7942 (t-170) cc_final: 0.7644 (t-170) REVERT: A 271 TYR cc_start: 0.8253 (t80) cc_final: 0.8035 (t80) REVERT: A 281 MET cc_start: 0.6972 (ppp) cc_final: 0.5405 (ptp) REVERT: B 36 GLU cc_start: 0.8560 (pm20) cc_final: 0.7875 (pm20) REVERT: B 39 LYS cc_start: 0.8324 (pttp) cc_final: 0.8085 (tptp) REVERT: B 106 TYR cc_start: 0.7466 (t80) cc_final: 0.7251 (t80) REVERT: C 274 ASP cc_start: 0.6995 (m-30) cc_final: 0.6217 (m-30) REVERT: C 281 MET cc_start: 0.6954 (pmm) cc_final: 0.6244 (pmm) REVERT: C 282 GLU cc_start: 0.5797 (mp0) cc_final: 0.5543 (mp0) REVERT: D 102 LYS cc_start: 0.5341 (tptp) cc_final: 0.5046 (tptm) REVERT: D 117 MET cc_start: 0.7586 (tpp) cc_final: 0.7363 (ttm) REVERT: E 164 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7169 (tt) REVERT: E 281 MET cc_start: 0.6825 (ppp) cc_final: 0.4978 (ptp) REVERT: F 36 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: G 274 ASP cc_start: 0.6904 (m-30) cc_final: 0.6560 (m-30) REVERT: G 281 MET cc_start: 0.6930 (pmm) cc_final: 0.6243 (pmm) REVERT: G 282 GLU cc_start: 0.5774 (mp0) cc_final: 0.5544 (mp0) REVERT: H 14 LYS cc_start: 0.7848 (tptp) cc_final: 0.7513 (pttp) outliers start: 34 outliers final: 25 residues processed: 211 average time/residue: 0.1275 time to fit residues: 38.5118 Evaluate side-chains 211 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN F 65 HIS F 118 HIS G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.193886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145273 restraints weight = 18068.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143043 restraints weight = 11822.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144369 restraints weight = 9581.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144813 restraints weight = 7852.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144857 restraints weight = 7295.051| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13680 Z= 0.125 Angle : 0.571 14.791 18518 Z= 0.280 Chirality : 0.039 0.191 2142 Planarity : 0.004 0.034 2220 Dihedral : 9.526 81.536 2306 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.38 % Favored : 93.12 % Rotamer: Outliers : 2.29 % Allowed : 17.55 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.22), residues: 1600 helix: 1.65 (0.16), residues: 1060 sheet: 0.54 (0.66), residues: 56 loop : -2.11 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 61 TYR 0.016 0.001 TYR H 106 PHE 0.014 0.001 PHE G 99 TRP 0.012 0.001 TRP E 96 HIS 0.010 0.001 HIS F 65 Details of bonding type rmsd covalent geometry : bond 0.00291 (13680) covalent geometry : angle 0.57084 (18518) hydrogen bonds : bond 0.04386 ( 748) hydrogen bonds : angle 3.50440 ( 2220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7261 (tt) REVERT: A 237 HIS cc_start: 0.7888 (t-170) cc_final: 0.7581 (t-170) REVERT: A 271 TYR cc_start: 0.8261 (t80) cc_final: 0.8056 (t80) REVERT: A 281 MET cc_start: 0.6931 (ppp) cc_final: 0.5331 (ptp) REVERT: B 36 GLU cc_start: 0.8548 (pm20) cc_final: 0.7863 (pm20) REVERT: B 39 LYS cc_start: 0.8326 (pttp) cc_final: 0.8079 (tptp) REVERT: C 274 ASP cc_start: 0.7107 (m-30) cc_final: 0.6320 (m-30) REVERT: C 281 MET cc_start: 0.6913 (pmm) cc_final: 0.6156 (pmm) REVERT: C 282 GLU cc_start: 0.5709 (mp0) cc_final: 0.5439 (mp0) REVERT: D 117 MET cc_start: 0.7601 (tpp) cc_final: 0.7312 (mtp) REVERT: E 164 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7269 (tt) REVERT: E 281 MET cc_start: 0.6819 (ppp) cc_final: 0.4937 (ptp) REVERT: F 36 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: F 68 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7443 (ttpt) REVERT: G 274 ASP cc_start: 0.7056 (m-30) cc_final: 0.6718 (m-30) REVERT: H 14 LYS cc_start: 0.7861 (tptp) cc_final: 0.7552 (pttp) outliers start: 31 outliers final: 26 residues processed: 216 average time/residue: 0.1287 time to fit residues: 39.8649 Evaluate side-chains 201 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN F 118 HIS G 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.189472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142948 restraints weight = 18093.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141109 restraints weight = 16535.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142557 restraints weight = 13030.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142687 restraints weight = 9178.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142757 restraints weight = 8604.358| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13680 Z= 0.204 Angle : 0.691 17.110 18518 Z= 0.335 Chirality : 0.042 0.168 2142 Planarity : 0.004 0.036 2220 Dihedral : 10.115 85.321 2306 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.94 % Favored : 92.56 % Rotamer: Outliers : 2.14 % Allowed : 17.92 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.22), residues: 1600 helix: 1.41 (0.16), residues: 1056 sheet: 0.32 (0.65), residues: 56 loop : -2.17 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 61 TYR 0.018 0.001 TYR H 106 PHE 0.018 0.001 PHE G 99 TRP 0.012 0.001 TRP C 134 HIS 0.012 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00500 (13680) covalent geometry : angle 0.69128 (18518) hydrogen bonds : bond 0.05702 ( 748) hydrogen bonds : angle 3.72302 ( 2220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7429 (tt) REVERT: A 237 HIS cc_start: 0.7880 (t-170) cc_final: 0.7576 (t-170) REVERT: A 281 MET cc_start: 0.6760 (ppp) cc_final: 0.4752 (ptp) REVERT: C 274 ASP cc_start: 0.7531 (m-30) cc_final: 0.7239 (m-30) REVERT: E 164 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7398 (tt) REVERT: E 281 MET cc_start: 0.6589 (ppp) cc_final: 0.4644 (ptp) REVERT: F 42 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8111 (mt-10) REVERT: F 68 LYS cc_start: 0.7660 (ttpp) cc_final: 0.7445 (ttpt) REVERT: G 274 ASP cc_start: 0.7362 (m-30) cc_final: 0.7093 (m-30) REVERT: H 14 LYS cc_start: 0.7946 (tptp) cc_final: 0.7709 (ptmm) outliers start: 29 outliers final: 25 residues processed: 208 average time/residue: 0.1229 time to fit residues: 36.6822 Evaluate side-chains 203 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 150 optimal weight: 0.0570 chunk 129 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN F 118 HIS G 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.190243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141266 restraints weight = 17921.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139219 restraints weight = 10975.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139684 restraints weight = 9564.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140673 restraints weight = 8904.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140657 restraints weight = 7595.779| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13680 Z= 0.175 Angle : 0.662 15.855 18518 Z= 0.320 Chirality : 0.041 0.170 2142 Planarity : 0.004 0.035 2220 Dihedral : 10.057 87.640 2306 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.00 % Favored : 92.50 % Rotamer: Outliers : 2.29 % Allowed : 17.63 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.22), residues: 1600 helix: 1.37 (0.16), residues: 1056 sheet: 0.28 (0.65), residues: 56 loop : -2.18 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 61 TYR 0.027 0.001 TYR H 106 PHE 0.017 0.001 PHE D 70 TRP 0.011 0.001 TRP E 96 HIS 0.007 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (13680) covalent geometry : angle 0.66157 (18518) hydrogen bonds : bond 0.05432 ( 748) hydrogen bonds : angle 3.72870 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.14 seconds wall clock time: 38 minutes 32.83 seconds (2312.83 seconds total)