Starting phenix.real_space_refine on Fri Jul 3 17:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8efv_28101/07_2026/8efv_28101.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efv_28101/07_2026/8efv_28101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8efv_28101/07_2026/8efv_28101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efv_28101/07_2026/8efv_28101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8efv_28101/07_2026/8efv_28101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efv_28101/07_2026/8efv_28101.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8efv_28101/07_2026/8efv_28101.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8efv_28101/07_2026/8efv_28101.cif" } resolution = 2.97 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= 0.003 sd= 0.095 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: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 4 5.21 5 S 26 5.16 5 C 9531 2.51 5 N 2769 2.21 5 O 2909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15295 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2324 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2355 Classifications: {'peptide': 301} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2453 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2442 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 293} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2345 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2340 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "H" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.32, per 1000 atoms: 0.22 Number of scatterers: 15295 At special positions: 0 Unit cell: (120.96, 135, 101.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 56 15.00 Mg 4 11.99 O 2909 8.00 N 2769 7.00 C 9531 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: 1.08 Conformation dependent library (CDL) restraints added in 525.7 milliseconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 19 sheets defined 57.3% alpha, 8.6% beta 17 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'D' and resid 17 through 34 removed outlier: 3.714A pdb=" N LYS D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 78 through 87 removed outlier: 3.681A pdb=" N ALA D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 removed outlier: 3.548A pdb=" N LEU D 102 " --> pdb=" O ILE D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 169 through 185 Processing helix chain 'D' and resid 189 through 199 removed outlier: 3.530A pdb=" N ARG D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 222 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 266 through 275 Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.561A pdb=" N LEU D 289 " --> pdb=" O HIS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'C' and resid 17 through 34 removed outlier: 3.800A pdb=" N LYS C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 78 through 88 removed outlier: 3.920A pdb=" N ALA C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 169 through 185 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.533A pdb=" N GLU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 222 Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.586A pdb=" N ILE C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.830A pdb=" N LEU C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'B' and resid 17 through 34 removed outlier: 3.720A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.511A pdb=" N HIS B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.663A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.740A pdb=" N GLU B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.962A pdb=" N GLU B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.552A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 222 Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 266 through 275 Processing helix chain 'B' and resid 277 through 285 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.509A pdb=" N LEU B 289 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'A' and resid 17 through 34 removed outlier: 3.598A pdb=" N LYS A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.762A pdb=" N LEU A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.601A pdb=" N LEU A 102 " --> pdb=" O ILE A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 109 through 116 removed outlier: 4.128A pdb=" N ALA A 113 " --> pdb=" O HIS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 203 through 221 removed outlier: 3.601A pdb=" N ALA A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 266 through 274 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'F' and resid 17 through 35 removed outlier: 3.821A pdb=" N LYS F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 79 through 86 Processing helix chain 'F' and resid 99 through 102 removed outlier: 3.561A pdb=" N LEU F 102 " --> pdb=" O ILE F 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 102' Processing helix chain 'F' and resid 106 through 116 removed outlier: 4.000A pdb=" N TYR F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Proline residue: F 112 - end of helix Processing helix chain 'F' and resid 147 through 151 removed outlier: 3.566A pdb=" N ILE F 151 " --> pdb=" O PRO F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.543A pdb=" N SER F 157 " --> pdb=" O PRO F 154 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 158 " --> pdb=" O LEU F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 158' Processing helix chain 'F' and resid 169 through 185 Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 203 through 221 removed outlier: 3.730A pdb=" N VAL F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA F 221 " --> pdb=" O PHE F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 246 through 261 removed outlier: 3.871A pdb=" N ARG F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 removed outlier: 4.376A pdb=" N ALA F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 285 through 292 Processing helix chain 'F' and resid 305 through 312 Processing helix chain 'E' and resid 22 through 35 Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 78 through 86 removed outlier: 3.671A pdb=" N ASN E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 109 through 115 removed outlier: 3.725A pdb=" N ALA E 113 " --> pdb=" O HIS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.604A pdb=" N ILE E 151 " --> pdb=" O PRO E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 169 through 185 Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.635A pdb=" N GLU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 222 Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 268 through 274 removed outlier: 3.581A pdb=" N THR E 272 " --> pdb=" O ALA E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 removed outlier: 3.857A pdb=" N LEU E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.819A pdb=" N ARG E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.063A pdb=" N ARG D 67 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP D 97 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR D 69 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP D 92 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE D 142 " --> pdb=" O ASP D 92 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 94 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA D 144 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE D 96 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU D 42 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 187 through 188 removed outlier: 7.270A pdb=" N ARG D 187 " --> pdb=" O ILE D 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 296 through 298 Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.362A pdb=" N LEU C 42 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 188 removed outlier: 7.281A pdb=" N ARG C 187 " --> pdb=" O ILE C 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.353A pdb=" N ARG B 67 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP B 97 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 69 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 42 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 123 Processing sheet with id=AA9, first strand: chain 'B' and resid 295 through 298 Processing sheet with id=AB1, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.302A pdb=" N LEU A 42 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 123 Processing sheet with id=AB3, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AB4, first strand: chain 'F' and resid 69 through 70 removed outlier: 3.668A pdb=" N ALA F 144 " --> pdb=" O ILE F 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'F' and resid 187 through 188 removed outlier: 7.325A pdb=" N ARG F 187 " --> pdb=" O ILE F 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 295 through 297 Processing sheet with id=AB8, first strand: chain 'E' and resid 69 through 70 removed outlier: 7.217A pdb=" N THR E 69 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU E 41 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR E 145 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU E 43 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU E 42 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 187 through 188 removed outlier: 7.233A pdb=" N ARG E 187 " --> pdb=" O ILE E 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 296 through 298 692 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5217 1.36 - 1.51: 4047 1.51 - 1.66: 6332 1.66 - 1.80: 42 1.80 - 1.95: 7 Bond restraints: 15645 Sorted by residual: bond pdb=" C3' DT G 20 " pdb=" C2' DT G 20 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.41e+00 bond pdb=" C3' DT H 9 " pdb=" C2' DT H 9 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" C3' DA H 18 " pdb=" C2' DA H 18 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.19e+00 bond pdb=" C3' DA G 14 " pdb=" C2' DA G 14 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.14e+00 bond pdb=" C3' DA H 14 " pdb=" C2' DA H 14 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.87e+00 ... (remaining 15640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 20729 1.50 - 3.00: 502 3.00 - 4.50: 105 4.50 - 6.00: 29 6.00 - 7.50: 9 Bond angle restraints: 21374 Sorted by residual: angle pdb=" N3 DT G 4 " pdb=" C4 DT G 4 " pdb=" O4 DT G 4 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT G 2 " pdb=" C4 DT G 2 " pdb=" O4 DT G 2 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT H 21 " pdb=" C4 DT H 21 " pdb=" O4 DT H 21 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT H 10 " pdb=" C4 DT H 10 " pdb=" O4 DT H 10 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT H 13 " pdb=" C4 DT H 13 " pdb=" O4 DT H 13 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 21369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 9066 34.01 - 68.03: 344 68.03 - 102.04: 19 102.04 - 136.05: 5 136.05 - 170.07: 2 Dihedral angle restraints: 9436 sinusoidal: 4262 harmonic: 5174 Sorted by residual: dihedral pdb=" O2A ADP A 400 " pdb=" O3A ADP A 400 " pdb=" PA ADP A 400 " pdb=" PB ADP A 400 " ideal model delta sinusoidal sigma weight residual 300.00 167.74 132.26 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" O1B ADP E 400 " pdb=" O3A ADP E 400 " pdb=" PB ADP E 400 " pdb=" PA ADP E 400 " ideal model delta sinusoidal sigma weight residual 300.00 178.00 122.00 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP F 400 " pdb=" O3A ADP F 400 " pdb=" PB ADP F 400 " pdb=" PA ADP F 400 " ideal model delta sinusoidal sigma weight residual -60.00 61.76 -121.77 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 9433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1596 0.031 - 0.062: 560 0.062 - 0.093: 170 0.093 - 0.124: 124 0.124 - 0.155: 7 Chirality restraints: 2457 Sorted by residual: chirality pdb=" C3' DG H 7 " pdb=" C4' DG H 7 " pdb=" O3' DG H 7 " pdb=" C2' DG H 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE D 290 " pdb=" N ILE D 290 " pdb=" C ILE D 290 " pdb=" CB ILE D 290 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" C3' DA G 3 " pdb=" C4' DA G 3 " pdb=" O3' DA G 3 " pdb=" C2' DA G 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 2454 not shown) Planarity restraints: 2607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 298 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO D 299 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 169 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO F 170 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 170 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 170 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 169 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 170 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.026 5.00e-02 4.00e+02 ... (remaining 2604 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 117 2.59 - 3.17: 11696 3.17 - 3.75: 23411 3.75 - 4.32: 32956 4.32 - 4.90: 55338 Nonbonded interactions: 123518 Sorted by model distance: nonbonded pdb=" OD1 ASP A 97 " pdb="MG MG A 401 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR F 52 " pdb=" O2B ADP F 400 " model vdw 2.177 3.040 nonbonded pdb=" O GLY D 293 " pdb=" OG1 THR D 305 " model vdw 2.191 3.040 nonbonded pdb=" ND1 HIS B 100 " pdb=" OG1 THR B 145 " model vdw 2.276 3.120 nonbonded pdb=" O LEU D 49 " pdb=" OH TYR D 168 " model vdw 2.280 3.040 ... (remaining 123513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'B' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'C' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 317)) selection = (chain 'D' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'E' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'F' and (resid 7 through 119 or resid 133 through 137 or (resid 138 and ( \ name N or name CA or name C or name O )) or resid 139 through 317)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.170 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15645 Z= 0.209 Angle : 0.600 7.501 21374 Z= 0.344 Chirality : 0.040 0.155 2457 Planarity : 0.005 0.047 2607 Dihedral : 16.910 170.067 6116 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1791 helix: 1.00 (0.17), residues: 955 sheet: 0.26 (0.37), residues: 216 loop : -0.01 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 310 TYR 0.008 0.001 TYR C 111 PHE 0.010 0.001 PHE A 211 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.21 (15645) covalent geometry : angle 0.60031 / 0.34 (21374) hydrogen bonds : bond 0.14997 / 9.76 ( 733) hydrogen bonds : angle 5.89193 / 4.18 ( 2056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.577 Fit side-chains REVERT: C 216 ASP cc_start: 0.8420 (m-30) cc_final: 0.8145 (m-30) REVERT: B 65 ASN cc_start: 0.8098 (m110) cc_final: 0.7794 (m-40) REVERT: B 191 GLU cc_start: 0.7989 (mp0) cc_final: 0.7777 (mp0) REVERT: B 310 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7966 (mtm-85) REVERT: A 204 MET cc_start: 0.8848 (tpp) cc_final: 0.8181 (tpt) REVERT: F 243 LEU cc_start: 0.7966 (mt) cc_final: 0.7757 (mt) REVERT: E 198 ARG cc_start: 0.7487 (mtt-85) cc_final: 0.7213 (mtt-85) outliers start: 0 outliers final: 1 residues processed: 220 average time/residue: 0.9027 time to fit residues: 212.5572 Evaluate side-chains 183 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.180898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140956 restraints weight = 15403.850| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.44 r_work: 0.3327 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15645 Z= 0.248 Angle : 0.725 9.083 21374 Z= 0.347 Chirality : 0.045 0.239 2457 Planarity : 0.006 0.061 2607 Dihedral : 17.167 173.876 2560 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.02 % Allowed : 9.04 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1791 helix: 0.88 (0.17), residues: 958 sheet: 0.12 (0.36), residues: 225 loop : -0.14 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 104 TYR 0.016 0.002 TYR C 111 PHE 0.015 0.002 PHE A 211 HIS 0.005 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.25 (15645) covalent geometry : angle 0.72519 / 0.35 (21374) hydrogen bonds : bond 0.05563 / 3.75 ( 733) hydrogen bonds : angle 4.74831 / 3.34 ( 2056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.373 Fit side-chains REVERT: D 163 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8317 (mm-30) REVERT: D 216 ASP cc_start: 0.8422 (m-30) cc_final: 0.7974 (m-30) REVERT: C 216 ASP cc_start: 0.8489 (m-30) cc_final: 0.8089 (m-30) REVERT: C 283 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: B 32 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7986 (mtmp) REVERT: B 65 ASN cc_start: 0.8402 (m110) cc_final: 0.8056 (m-40) REVERT: B 191 GLU cc_start: 0.8159 (mp0) cc_final: 0.7858 (mp0) REVERT: F 243 LEU cc_start: 0.7607 (mt) cc_final: 0.7339 (mt) REVERT: E 119 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6222 (ttt) REVERT: E 198 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7374 (mtt-85) outliers start: 15 outliers final: 5 residues processed: 182 average time/residue: 0.8298 time to fit residues: 161.5763 Evaluate side-chains 176 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain E residue 119 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 182 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143566 restraints weight = 15635.378| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.44 r_work: 0.3357 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15645 Z= 0.146 Angle : 0.615 8.311 21374 Z= 0.296 Chirality : 0.041 0.221 2457 Planarity : 0.005 0.060 2607 Dihedral : 16.930 171.427 2558 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.36 % Allowed : 11.28 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1791 helix: 1.13 (0.17), residues: 954 sheet: 0.11 (0.35), residues: 225 loop : -0.11 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 19 TYR 0.011 0.001 TYR C 111 PHE 0.012 0.001 PHE B 117 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (15645) covalent geometry : angle 0.61460 / 0.30 (21374) hydrogen bonds : bond 0.04271 / 2.86 ( 733) hydrogen bonds : angle 4.38299 / 3.08 ( 2056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.599 Fit side-chains REVERT: D 163 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8317 (mm-30) REVERT: D 216 ASP cc_start: 0.8411 (m-30) cc_final: 0.7934 (m-30) REVERT: C 216 ASP cc_start: 0.8469 (m-30) cc_final: 0.8103 (m-30) REVERT: C 310 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8464 (mtm-85) REVERT: B 65 ASN cc_start: 0.8404 (m110) cc_final: 0.8121 (m-40) REVERT: B 191 GLU cc_start: 0.8186 (mp0) cc_final: 0.7936 (mp0) REVERT: B 216 ASP cc_start: 0.8636 (m-30) cc_final: 0.8426 (m-30) REVERT: A 9 LYS cc_start: 0.8247 (ptpp) cc_final: 0.7874 (ptpt) REVERT: A 228 ARG cc_start: 0.7889 (ttt-90) cc_final: 0.7681 (ttt-90) REVERT: A 312 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7701 (mp) REVERT: F 243 LEU cc_start: 0.7601 (mt) cc_final: 0.7351 (mt) REVERT: E 119 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6342 (ttt) REVERT: E 198 ARG cc_start: 0.7703 (mtt-85) cc_final: 0.7367 (mtt-85) REVERT: E 276 GLU cc_start: 0.5721 (tp30) cc_final: 0.5426 (tp30) outliers start: 20 outliers final: 5 residues processed: 188 average time/residue: 0.8148 time to fit residues: 164.6996 Evaluate side-chains 170 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain E residue 119 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 171 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.181868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141511 restraints weight = 15633.448| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.47 r_work: 0.3350 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15645 Z= 0.176 Angle : 0.650 9.779 21374 Z= 0.309 Chirality : 0.042 0.227 2457 Planarity : 0.006 0.062 2607 Dihedral : 16.851 172.693 2558 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.36 % Allowed : 12.64 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1791 helix: 1.13 (0.17), residues: 953 sheet: 0.06 (0.35), residues: 225 loop : -0.16 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 19 TYR 0.013 0.001 TYR C 111 PHE 0.013 0.002 PHE A 211 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (15645) covalent geometry : angle 0.64998 / 0.31 (21374) hydrogen bonds : bond 0.04351 / 2.95 ( 733) hydrogen bonds : angle 4.31568 / 3.03 ( 2056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.586 Fit side-chains REVERT: D 163 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8284 (mm-30) REVERT: D 216 ASP cc_start: 0.8445 (m-30) cc_final: 0.8006 (m-30) REVERT: D 307 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 216 ASP cc_start: 0.8454 (m-30) cc_final: 0.8065 (m-30) REVERT: C 310 ARG cc_start: 0.8677 (ttp80) cc_final: 0.8417 (mtm-85) REVERT: B 65 ASN cc_start: 0.8438 (m110) cc_final: 0.8139 (m-40) REVERT: B 191 GLU cc_start: 0.8220 (mp0) cc_final: 0.7913 (mp0) REVERT: A 9 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7888 (ptpt) REVERT: A 147 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7951 (mtp85) REVERT: A 312 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7613 (mp) REVERT: F 243 LEU cc_start: 0.7768 (mt) cc_final: 0.7546 (mt) REVERT: E 119 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6322 (ttt) REVERT: E 198 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7303 (mtt-85) REVERT: E 276 GLU cc_start: 0.5616 (tp30) cc_final: 0.5341 (tp30) outliers start: 20 outliers final: 9 residues processed: 184 average time/residue: 0.8607 time to fit residues: 169.8442 Evaluate side-chains 175 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 153 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 154 optimal weight: 0.0020 chunk 89 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 151 optimal weight: 0.0970 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN E 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.185333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145790 restraints weight = 15572.608| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.44 r_work: 0.3294 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15645 Z= 0.106 Angle : 0.578 10.240 21374 Z= 0.278 Chirality : 0.039 0.217 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.620 170.399 2558 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.50 % Allowed : 13.66 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1791 helix: 1.40 (0.17), residues: 953 sheet: 0.07 (0.35), residues: 225 loop : 0.03 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 19 TYR 0.008 0.001 TYR C 111 PHE 0.009 0.001 PHE B 211 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (15645) covalent geometry : angle 0.57813 / 0.28 (21374) hydrogen bonds : bond 0.03510 / 2.35 ( 733) hydrogen bonds : angle 4.11734 / 2.88 ( 2056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.584 Fit side-chains REVERT: D 163 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8237 (mm-30) REVERT: C 216 ASP cc_start: 0.8287 (m-30) cc_final: 0.7944 (m-30) REVERT: C 280 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8807 (t) REVERT: B 65 ASN cc_start: 0.8407 (m110) cc_final: 0.8082 (m-40) REVERT: B 191 GLU cc_start: 0.8135 (mp0) cc_final: 0.7569 (mp0) REVERT: B 216 ASP cc_start: 0.8573 (m-30) cc_final: 0.8367 (m-30) REVERT: A 9 LYS cc_start: 0.8197 (ptpp) cc_final: 0.7853 (ptpt) REVERT: A 312 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7383 (mp) REVERT: F 199 ARG cc_start: 0.8153 (mpt90) cc_final: 0.7591 (mmt-90) REVERT: F 248 ARG cc_start: 0.7444 (mtt90) cc_final: 0.6829 (mmm160) REVERT: E 36 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: E 115 GLU cc_start: 0.7804 (mp0) cc_final: 0.7528 (mp0) REVERT: E 198 ARG cc_start: 0.7456 (mtt-85) cc_final: 0.7089 (mtt-85) outliers start: 22 outliers final: 8 residues processed: 193 average time/residue: 0.8490 time to fit residues: 176.2546 Evaluate side-chains 178 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 20 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140275 restraints weight = 15468.973| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.44 r_work: 0.3355 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15645 Z= 0.178 Angle : 0.647 8.861 21374 Z= 0.308 Chirality : 0.042 0.231 2457 Planarity : 0.006 0.063 2607 Dihedral : 16.692 172.830 2558 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.38 % Allowed : 14.41 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1791 helix: 1.25 (0.17), residues: 954 sheet: 0.05 (0.35), residues: 225 loop : -0.10 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 19 TYR 0.015 0.001 TYR C 111 PHE 0.013 0.002 PHE A 211 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (15645) covalent geometry : angle 0.64742 / 0.31 (21374) hydrogen bonds : bond 0.04215 / 2.88 ( 733) hydrogen bonds : angle 4.18691 / 2.95 ( 2056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.606 Fit side-chains REVERT: D 163 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8282 (mm-30) REVERT: D 307 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7849 (mt) REVERT: C 216 ASP cc_start: 0.8416 (m-30) cc_final: 0.8012 (m-30) REVERT: B 32 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7957 (mtmp) REVERT: B 65 ASN cc_start: 0.8470 (m110) cc_final: 0.8178 (m-40) REVERT: B 191 GLU cc_start: 0.8197 (mp0) cc_final: 0.7888 (mp0) REVERT: A 147 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7921 (mtp85) REVERT: A 312 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7543 (mp) REVERT: F 199 ARG cc_start: 0.8319 (mpt90) cc_final: 0.7811 (mmt-90) REVERT: F 248 ARG cc_start: 0.7453 (mtt90) cc_final: 0.6947 (mmm160) REVERT: E 198 ARG cc_start: 0.7594 (mtt-85) cc_final: 0.7254 (mtt-85) REVERT: E 276 GLU cc_start: 0.5482 (tp30) cc_final: 0.5207 (tp30) outliers start: 35 outliers final: 14 residues processed: 190 average time/residue: 0.8680 time to fit residues: 176.9320 Evaluate side-chains 180 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 296 LYS Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.179469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139040 restraints weight = 15488.500| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.46 r_work: 0.3169 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15645 Z= 0.236 Angle : 0.716 10.417 21374 Z= 0.341 Chirality : 0.045 0.232 2457 Planarity : 0.006 0.061 2607 Dihedral : 16.853 172.683 2558 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.24 % Allowed : 15.09 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1791 helix: 0.93 (0.17), residues: 961 sheet: -0.05 (0.34), residues: 223 loop : -0.32 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 228 TYR 0.016 0.001 TYR C 111 PHE 0.016 0.002 PHE A 211 HIS 0.005 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 (15645) covalent geometry : angle 0.71642 / 0.34 (21374) hydrogen bonds : bond 0.04795 / 3.29 ( 733) hydrogen bonds : angle 4.33235 / 3.05 ( 2056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.581 Fit side-chains REVERT: D 163 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 216 ASP cc_start: 0.8482 (m-30) cc_final: 0.8073 (m-30) REVERT: B 32 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7889 (mtmp) REVERT: B 65 ASN cc_start: 0.8439 (m110) cc_final: 0.8123 (m-40) REVERT: B 191 GLU cc_start: 0.8138 (mp0) cc_final: 0.7561 (mp0) REVERT: B 300 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7309 (mtm-85) REVERT: A 147 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7952 (mtp85) REVERT: A 312 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7425 (mp) REVERT: F 243 LEU cc_start: 0.7657 (mm) cc_final: 0.7311 (mt) REVERT: E 119 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6348 (ttt) REVERT: E 198 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.7163 (mtt-85) REVERT: E 276 GLU cc_start: 0.5489 (tp30) cc_final: 0.5156 (tp30) outliers start: 33 outliers final: 18 residues processed: 186 average time/residue: 0.8444 time to fit residues: 169.2310 Evaluate side-chains 179 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 296 LYS Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 121 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 109 HIS F 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.184015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143827 restraints weight = 15594.418| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.48 r_work: 0.3234 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15645 Z= 0.112 Angle : 0.599 12.473 21374 Z= 0.289 Chirality : 0.039 0.219 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.634 169.735 2558 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.63 % Allowed : 16.04 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1791 helix: 1.31 (0.17), residues: 954 sheet: -0.00 (0.35), residues: 225 loop : -0.11 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 228 TYR 0.008 0.001 TYR C 111 PHE 0.012 0.001 PHE B 117 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15645) covalent geometry : angle 0.59895 / 0.29 (21374) hydrogen bonds : bond 0.03520 / 2.36 ( 733) hydrogen bonds : angle 4.11890 / 2.89 ( 2056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.586 Fit side-chains REVERT: D 32 LYS cc_start: 0.7163 (mttp) cc_final: 0.6884 (mmpt) REVERT: D 163 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8206 (mm-30) REVERT: D 230 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7679 (tpp-160) REVERT: C 216 ASP cc_start: 0.8322 (m-30) cc_final: 0.7964 (m-30) REVERT: C 280 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8770 (t) REVERT: B 65 ASN cc_start: 0.8432 (m110) cc_final: 0.8111 (m-40) REVERT: B 191 GLU cc_start: 0.8142 (mp0) cc_final: 0.7565 (mp0) REVERT: A 147 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7949 (mtp85) REVERT: A 283 GLU cc_start: 0.8311 (mp0) cc_final: 0.8096 (mt-10) REVERT: A 312 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7338 (mp) REVERT: F 199 ARG cc_start: 0.8077 (mpt90) cc_final: 0.7525 (mmt-90) REVERT: E 115 GLU cc_start: 0.7939 (mp0) cc_final: 0.7333 (mp0) REVERT: E 198 ARG cc_start: 0.7410 (mtt-85) cc_final: 0.7170 (mtp85) REVERT: E 276 GLU cc_start: 0.5388 (tp30) cc_final: 0.5119 (tp30) outliers start: 24 outliers final: 11 residues processed: 185 average time/residue: 0.8325 time to fit residues: 166.4009 Evaluate side-chains 179 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.181837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141683 restraints weight = 15406.988| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.46 r_work: 0.3245 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15645 Z= 0.165 Angle : 0.644 12.107 21374 Z= 0.308 Chirality : 0.042 0.230 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.683 171.844 2558 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.63 % Allowed : 16.59 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1791 helix: 1.24 (0.17), residues: 954 sheet: -0.02 (0.35), residues: 225 loop : -0.19 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 228 TYR 0.014 0.001 TYR C 111 PHE 0.012 0.001 PHE A 211 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (15645) covalent geometry : angle 0.64448 / 0.31 (21374) hydrogen bonds : bond 0.03961 / 2.69 ( 733) hydrogen bonds : angle 4.16252 / 2.93 ( 2056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.541 Fit side-chains REVERT: D 32 LYS cc_start: 0.7189 (mttp) cc_final: 0.6903 (mmpt) REVERT: D 163 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8220 (mm-30) REVERT: C 216 ASP cc_start: 0.8349 (m-30) cc_final: 0.7985 (m-30) REVERT: B 65 ASN cc_start: 0.8421 (m110) cc_final: 0.8118 (m-40) REVERT: B 191 GLU cc_start: 0.8138 (mp0) cc_final: 0.7552 (mp0) REVERT: A 147 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7965 (mtp85) REVERT: A 283 GLU cc_start: 0.8320 (mp0) cc_final: 0.8104 (mt-10) REVERT: A 312 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7313 (mp) REVERT: F 199 ARG cc_start: 0.8073 (mpt90) cc_final: 0.7541 (mmt-90) REVERT: E 115 GLU cc_start: 0.8082 (mp0) cc_final: 0.7532 (mp0) REVERT: E 119 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6406 (ttt) REVERT: E 198 ARG cc_start: 0.7454 (mtt-85) cc_final: 0.7080 (mtt-85) REVERT: E 276 GLU cc_start: 0.5498 (tp30) cc_final: 0.5159 (tp30) outliers start: 24 outliers final: 16 residues processed: 180 average time/residue: 0.8562 time to fit residues: 165.5781 Evaluate side-chains 181 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 21 optimal weight: 6.9990 chunk 99 optimal weight: 0.0050 chunk 163 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 152 optimal weight: 8.9990 chunk 56 optimal weight: 0.0010 chunk 139 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN F 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.185484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.146011 restraints weight = 15525.851| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.49 r_work: 0.3338 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15645 Z= 0.105 Angle : 0.590 13.178 21374 Z= 0.285 Chirality : 0.039 0.220 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.519 169.460 2558 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.09 % Allowed : 17.06 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1791 helix: 1.49 (0.17), residues: 954 sheet: 0.02 (0.35), residues: 225 loop : 0.04 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 228 TYR 0.007 0.001 TYR C 111 PHE 0.010 0.001 PHE B 117 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (15645) covalent geometry : angle 0.58983 / 0.29 (21374) hydrogen bonds : bond 0.03244 / 2.17 ( 733) hydrogen bonds : angle 4.02268 / 2.82 ( 2056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.448 Fit side-chains REVERT: D 163 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8191 (mm-30) REVERT: C 216 ASP cc_start: 0.8153 (m-30) cc_final: 0.7819 (m-30) REVERT: C 280 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8775 (t) REVERT: B 65 ASN cc_start: 0.8295 (m110) cc_final: 0.7958 (m-40) REVERT: B 92 ASP cc_start: 0.8397 (p0) cc_final: 0.7900 (m-30) REVERT: B 191 GLU cc_start: 0.8096 (mp0) cc_final: 0.7523 (mp0) REVERT: A 147 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: A 283 GLU cc_start: 0.8277 (mp0) cc_final: 0.8059 (mt-10) REVERT: F 199 ARG cc_start: 0.8098 (mpt90) cc_final: 0.7650 (mmt-90) REVERT: F 248 ARG cc_start: 0.7475 (mtt90) cc_final: 0.6883 (mmm160) REVERT: E 115 GLU cc_start: 0.8069 (mp0) cc_final: 0.7564 (mp0) REVERT: E 198 ARG cc_start: 0.7406 (mtt-85) cc_final: 0.7133 (mtp85) outliers start: 16 outliers final: 11 residues processed: 179 average time/residue: 0.8203 time to fit residues: 157.6963 Evaluate side-chains 175 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144147 restraints weight = 15324.346| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.43 r_work: 0.3363 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15645 Z= 0.138 Angle : 0.621 12.335 21374 Z= 0.299 Chirality : 0.040 0.228 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.554 171.366 2558 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.09 % Allowed : 17.00 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 1791 helix: 1.43 (0.17), residues: 954 sheet: 0.04 (0.35), residues: 225 loop : 0.01 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 228 TYR 0.012 0.001 TYR C 111 PHE 0.010 0.001 PHE A 44 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (15645) covalent geometry : angle 0.62136 / 0.30 (21374) hydrogen bonds : bond 0.03596 / 2.44 ( 733) hydrogen bonds : angle 4.06709 / 2.87 ( 2056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5448.12 seconds wall clock time: 93 minutes 28.11 seconds (5608.11 seconds total)