Starting phenix.real_space_refine on Thu Aug 6 12:17:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8efv_28101/08_2026/8efv_28101.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efv_28101/08_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_28101/08_2026/8efv_28101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efv_28101/08_2026/8efv_28101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8efv_28101/08_2026/8efv_28101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efv_28101/08_2026/8efv_28101.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8efv_28101/08_2026/8efv_28101.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8efv_28101/08_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.45, per 1000 atoms: 0.23 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: 1.37 Conformation dependent library (CDL) restraints added in 543.5 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: 1.80 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: 2.57 Time building geometry restraints manager: 1.75 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: 20728 1.50 - 3.00: 502 3.00 - 4.50: 106 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.220 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- 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 : 0.601 7.501 21374 Z= 0.345 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 0.60102 / 0.35 (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 : 0.581 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: 0.8550 time to fit residues: 201.4114 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 : 0.527 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.178655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139334 restraints weight = 15428.800| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.39 r_work: 0.3323 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15645 Z= 0.252 Angle : 0.735 9.269 21374 Z= 0.351 Chirality : 0.046 0.251 2457 Planarity : 0.006 0.062 2607 Dihedral : 17.160 173.347 2560 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.22 % Allowed : 9.11 % Favored : 89.67 % 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: 0.54 (0.20), residues: 1791 helix: 0.83 (0.17), residues: 964 sheet: 0.16 (0.36), residues: 223 loop : -0.12 (0.25), residues: 604 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 0.006 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.25 (15645) covalent geometry : angle 0.73480 / 0.35 (21374) hydrogen bonds : bond 0.05359 / 3.63 ( 733) hydrogen bonds : angle 4.71554 / 3.32 ( 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 195 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.442 Fit side-chains REVERT: D 216 ASP cc_start: 0.8465 (m-30) cc_final: 0.7999 (m-30) REVERT: C 216 ASP cc_start: 0.8532 (m-30) cc_final: 0.8135 (m-30) REVERT: C 283 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: B 32 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8015 (mtmp) REVERT: B 65 ASN cc_start: 0.8431 (m110) cc_final: 0.8113 (m-40) REVERT: B 138 ARG cc_start: 0.8403 (ttt180) cc_final: 0.8197 (ttt180) REVERT: B 191 GLU cc_start: 0.8197 (mp0) cc_final: 0.7911 (mp0) REVERT: A 312 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7764 (mp) REVERT: F 243 LEU cc_start: 0.7675 (mt) cc_final: 0.7408 (mt) REVERT: E 119 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6264 (ttt) REVERT: E 198 ARG cc_start: 0.7789 (mtt-85) cc_final: 0.7469 (mtt-85) outliers start: 18 outliers final: 6 residues processed: 183 average time/residue: 0.8044 time to fit residues: 158.3515 Evaluate side-chains 176 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR 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 A residue 312 LEU 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: 0.9980 chunk 6 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.183070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143229 restraints weight = 15633.685| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.47 r_work: 0.3329 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15645 Z= 0.147 Angle : 0.619 8.503 21374 Z= 0.298 Chirality : 0.041 0.243 2457 Planarity : 0.005 0.060 2607 Dihedral : 16.915 170.680 2558 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.36 % Allowed : 11.49 % Favored : 87.15 % 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: 0.78 (0.20), residues: 1791 helix: 1.12 (0.17), residues: 954 sheet: 0.09 (0.35), residues: 225 loop : -0.12 (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 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (15645) covalent geometry : angle 0.61873 / 0.30 (21374) hydrogen bonds : bond 0.04294 / 2.88 ( 733) hydrogen bonds : angle 4.38288 / 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 198 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.529 Fit side-chains REVERT: D 216 ASP cc_start: 0.8379 (m-30) cc_final: 0.7945 (m-30) REVERT: C 216 ASP cc_start: 0.8439 (m-30) cc_final: 0.8055 (m-30) REVERT: C 283 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: B 65 ASN cc_start: 0.8390 (m110) cc_final: 0.8095 (m-40) REVERT: B 191 GLU cc_start: 0.8120 (mp0) cc_final: 0.7848 (mp0) REVERT: B 216 ASP cc_start: 0.8617 (m-30) cc_final: 0.8412 (m-30) REVERT: A 9 LYS cc_start: 0.8228 (ptpp) cc_final: 0.7857 (ptpt) REVERT: A 312 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7632 (mp) REVERT: F 147 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.8016 (mtp180) REVERT: F 243 LEU cc_start: 0.7579 (mt) cc_final: 0.7331 (mt) REVERT: E 119 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6318 (ttt) REVERT: E 198 ARG cc_start: 0.7651 (mtt-85) cc_final: 0.7296 (mtt-85) REVERT: E 276 GLU cc_start: 0.5677 (tp30) cc_final: 0.5386 (tp30) outliers start: 20 outliers final: 5 residues processed: 185 average time/residue: 0.7643 time to fit residues: 151.8414 Evaluate side-chains 168 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain E residue 290 ILE 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: 0.8980 chunk 165 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.182473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142723 restraints weight = 15625.253| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.43 r_work: 0.3351 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15645 Z= 0.156 Angle : 0.631 9.865 21374 Z= 0.300 Chirality : 0.041 0.248 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.794 171.659 2558 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.36 % Allowed : 13.19 % Favored : 85.45 % 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: 1.18 (0.17), residues: 954 sheet: 0.06 (0.35), residues: 225 loop : -0.12 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 19 TYR 0.012 0.001 TYR C 111 PHE 0.012 0.001 PHE A 211 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (15645) covalent geometry : angle 0.63093 / 0.30 (21374) hydrogen bonds : bond 0.04153 / 2.81 ( 733) hydrogen bonds : angle 4.27061 / 3.00 ( 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 192 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.536 Fit side-chains REVERT: D 216 ASP cc_start: 0.8447 (m-30) cc_final: 0.7990 (m-30) REVERT: D 307 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 216 ASP cc_start: 0.8479 (m-30) cc_final: 0.8079 (m-30) REVERT: B 65 ASN cc_start: 0.8444 (m110) cc_final: 0.8165 (m-40) REVERT: B 191 GLU cc_start: 0.8246 (mp0) cc_final: 0.7957 (mp0) REVERT: A 9 LYS cc_start: 0.8237 (ptpp) cc_final: 0.7877 (ptpt) REVERT: A 147 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8004 (mtp85) REVERT: A 312 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7683 (mp) REVERT: F 147 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.8010 (mtp180) REVERT: F 243 LEU cc_start: 0.7812 (mt) cc_final: 0.7590 (mt) REVERT: E 119 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6365 (ttt) REVERT: E 198 ARG cc_start: 0.7699 (mtt-85) cc_final: 0.7360 (mtt-85) REVERT: E 276 GLU cc_start: 0.5717 (tp30) cc_final: 0.5439 (tp30) outliers start: 20 outliers final: 10 residues processed: 181 average time/residue: 0.7871 time to fit residues: 152.8735 Evaluate side-chains 175 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 115 optimal weight: 0.0010 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 105 optimal weight: 0.0980 chunk 154 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.186096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148141 restraints weight = 15662.428| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.44 r_work: 0.3373 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1281 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= 0.105 Angle : 0.576 10.370 21374 Z= 0.277 Chirality : 0.039 0.241 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.574 169.721 2558 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.56 % Allowed : 13.60 % 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: 1.11 (0.20), residues: 1791 helix: 1.43 (0.17), residues: 953 sheet: 0.09 (0.35), residues: 225 loop : 0.04 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.00229 / 0.10 (15645) covalent geometry : angle 0.57640 / 0.28 (21374) hydrogen bonds : bond 0.03459 / 2.32 ( 733) hydrogen bonds : angle 4.08676 / 2.86 ( 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 206 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.489 Fit side-chains REVERT: D 32 LYS cc_start: 0.7267 (mttp) cc_final: 0.6979 (mmpt) REVERT: C 216 ASP cc_start: 0.8262 (m-30) cc_final: 0.7918 (m-30) REVERT: C 280 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8782 (t) REVERT: B 65 ASN cc_start: 0.8346 (m110) cc_final: 0.8027 (m-40) REVERT: B 191 GLU cc_start: 0.8145 (mp0) cc_final: 0.7811 (mp0) REVERT: A 9 LYS cc_start: 0.8175 (ptpp) cc_final: 0.7809 (ptpt) REVERT: A 312 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7421 (mp) REVERT: F 147 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7919 (mtp180) REVERT: F 199 ARG cc_start: 0.8240 (mpt90) cc_final: 0.7675 (mmt-90) REVERT: F 248 ARG cc_start: 0.7488 (mtt90) cc_final: 0.6946 (mmm160) REVERT: E 36 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: E 115 GLU cc_start: 0.7958 (mp0) cc_final: 0.7731 (mp0) REVERT: E 198 ARG cc_start: 0.7466 (mtt-85) cc_final: 0.7215 (mtp85) outliers start: 23 outliers final: 7 residues processed: 196 average time/residue: 0.7333 time to fit residues: 154.7415 Evaluate side-chains 178 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 106 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.183162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143603 restraints weight = 15472.641| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.43 r_work: 0.3307 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15645 Z= 0.150 Angle : 0.615 9.477 21374 Z= 0.293 Chirality : 0.041 0.249 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.598 171.612 2558 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.97 % Allowed : 15.09 % Favored : 82.94 % 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: 1.01 (0.20), residues: 1791 helix: 1.35 (0.17), residues: 955 sheet: 0.08 (0.35), residues: 225 loop : -0.02 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 19 TYR 0.013 0.001 TYR C 111 PHE 0.011 0.001 PHE A 211 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (15645) covalent geometry : angle 0.61504 / 0.29 (21374) hydrogen bonds : bond 0.03863 / 2.63 ( 733) hydrogen bonds : angle 4.10977 / 2.89 ( 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 200 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.565 Fit side-chains REVERT: D 32 LYS cc_start: 0.7287 (mttp) cc_final: 0.6997 (mmpt) REVERT: C 216 ASP cc_start: 0.8283 (m-30) cc_final: 0.7879 (m-30) REVERT: C 280 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8778 (t) REVERT: B 65 ASN cc_start: 0.8412 (m110) cc_final: 0.8089 (m-40) REVERT: B 191 GLU cc_start: 0.8085 (mp0) cc_final: 0.7514 (mp0) REVERT: A 9 LYS cc_start: 0.8183 (ptpp) cc_final: 0.7975 (ptpt) REVERT: A 147 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7747 (mtp85) REVERT: A 312 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7390 (mp) REVERT: F 147 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7928 (mtp180) REVERT: F 199 ARG cc_start: 0.8160 (mpt90) cc_final: 0.7583 (mmt-90) REVERT: F 248 ARG cc_start: 0.7448 (mtt90) cc_final: 0.6879 (mmm160) REVERT: E 115 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: E 198 ARG cc_start: 0.7452 (mtt-85) cc_final: 0.7104 (mtt-85) REVERT: E 276 GLU cc_start: 0.5376 (tp30) cc_final: 0.5126 (tp30) REVERT: E 297 ARG cc_start: 0.6663 (mmm-85) cc_final: 0.6442 (mmm-85) outliers start: 29 outliers final: 14 residues processed: 191 average time/residue: 0.7364 time to fit residues: 151.2034 Evaluate side-chains 187 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 242 GLU Chi-restraints excluded: chain E residue 115 GLU 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: 0.9990 chunk 13 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 115 optimal weight: 0.0000 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.182097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141779 restraints weight = 15468.713| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.48 r_work: 0.3204 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15645 Z= 0.164 Angle : 0.636 10.844 21374 Z= 0.303 Chirality : 0.042 0.252 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.647 171.432 2558 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.63 % Allowed : 15.30 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1791 helix: 1.28 (0.17), residues: 954 sheet: 0.03 (0.35), residues: 225 loop : -0.12 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 19 TYR 0.013 0.001 TYR C 111 PHE 0.013 0.001 PHE A 211 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.16 (15645) covalent geometry : angle 0.63561 / 0.30 (21374) hydrogen bonds : bond 0.04040 / 2.76 ( 733) hydrogen bonds : angle 4.14907 / 2.92 ( 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 198 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.395 Fit side-chains REVERT: C 216 ASP cc_start: 0.8359 (m-30) cc_final: 0.7979 (m-30) REVERT: B 65 ASN cc_start: 0.8422 (m110) cc_final: 0.8094 (m-40) REVERT: B 191 GLU cc_start: 0.8143 (mp0) cc_final: 0.7566 (mp0) REVERT: A 147 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7864 (mtp85) REVERT: A 283 GLU cc_start: 0.8361 (mp0) cc_final: 0.8115 (mt-10) REVERT: A 312 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7410 (mp) REVERT: F 199 ARG cc_start: 0.8184 (mpt90) cc_final: 0.7651 (mmt-90) REVERT: F 243 LEU cc_start: 0.7682 (mm) cc_final: 0.7387 (mt) REVERT: E 115 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: E 198 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7152 (mtt-85) REVERT: E 276 GLU cc_start: 0.5481 (tp30) cc_final: 0.5201 (tp30) outliers start: 24 outliers final: 16 residues processed: 188 average time/residue: 0.6801 time to fit residues: 137.4385 Evaluate side-chains 186 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 296 LYS Chi-restraints excluded: chain C residue 36 GLU 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 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 F residue 227 THR Chi-restraints excluded: chain E residue 115 GLU 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: 0.8980 chunk 2 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.184350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144232 restraints weight = 15613.765| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.48 r_work: 0.3280 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15645 Z= 0.114 Angle : 0.593 12.057 21374 Z= 0.285 Chirality : 0.039 0.244 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.551 170.059 2558 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.90 % Allowed : 15.50 % Favored : 82.60 % 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: 1.11 (0.20), residues: 1791 helix: 1.45 (0.17), residues: 954 sheet: 0.08 (0.35), residues: 225 loop : -0.00 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 228 TYR 0.010 0.001 TYR C 111 PHE 0.010 0.001 PHE B 117 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (15645) covalent geometry : angle 0.59312 / 0.29 (21374) hydrogen bonds : bond 0.03497 / 2.36 ( 733) hydrogen bonds : angle 4.04091 / 2.83 ( 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 202 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.353 Fit side-chains REVERT: D 32 LYS cc_start: 0.7151 (mttp) cc_final: 0.6883 (mmpt) REVERT: D 230 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7676 (tpp-160) REVERT: D 307 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7727 (mt) REVERT: C 216 ASP cc_start: 0.8266 (m-30) cc_final: 0.7912 (m-30) REVERT: C 280 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8797 (t) REVERT: B 32 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7824 (mtmp) REVERT: B 65 ASN cc_start: 0.8417 (m110) cc_final: 0.8086 (m-40) REVERT: B 191 GLU cc_start: 0.8174 (mp0) cc_final: 0.7838 (mp0) REVERT: A 147 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7813 (mtp85) REVERT: A 283 GLU cc_start: 0.8327 (mp0) cc_final: 0.8091 (mt-10) REVERT: F 199 ARG cc_start: 0.8096 (mpt90) cc_final: 0.7637 (mmt-90) REVERT: E 115 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: E 119 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6362 (ttt) REVERT: E 198 ARG cc_start: 0.7447 (mtt-85) cc_final: 0.7162 (mtp85) REVERT: E 276 GLU cc_start: 0.5343 (tp30) cc_final: 0.5093 (tp30) outliers start: 28 outliers final: 12 residues processed: 189 average time/residue: 0.6868 time to fit residues: 139.7567 Evaluate side-chains 185 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 32 LYS 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 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 115 GLU Chi-restraints excluded: chain E residue 119 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 132 optimal weight: 0.0060 chunk 145 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.185494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.146060 restraints weight = 15426.440| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.44 r_work: 0.3344 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.002 0.042 15645 Z= 0.109 Angle : 0.584 12.383 21374 Z= 0.281 Chirality : 0.039 0.246 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.465 170.238 2558 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.50 % Allowed : 16.18 % 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: 1.22 (0.20), residues: 1791 helix: 1.53 (0.17), residues: 951 sheet: 0.09 (0.35), residues: 225 loop : 0.09 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 228 TYR 0.009 0.001 TYR C 111 PHE 0.009 0.001 PHE A 44 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15645) covalent geometry : angle 0.58445 / 0.28 (21374) hydrogen bonds : bond 0.03318 / 2.24 ( 733) hydrogen bonds : angle 3.98182 / 2.79 ( 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 196 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.524 Fit side-chains REVERT: D 230 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.7778 (tpp-160) REVERT: D 307 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7758 (mt) REVERT: C 216 ASP cc_start: 0.8171 (m-30) cc_final: 0.7825 (m-30) REVERT: C 280 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8806 (t) REVERT: B 65 ASN cc_start: 0.8339 (m110) cc_final: 0.8001 (m-40) REVERT: B 191 GLU cc_start: 0.8139 (mp0) cc_final: 0.7587 (mp0) REVERT: A 147 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7778 (mtp85) REVERT: A 283 GLU cc_start: 0.8295 (mp0) cc_final: 0.8074 (mt-10) REVERT: A 312 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7369 (mp) REVERT: F 199 ARG cc_start: 0.8166 (mpt90) cc_final: 0.7642 (mmt-90) REVERT: F 248 ARG cc_start: 0.7465 (mtt90) cc_final: 0.6920 (mmm160) REVERT: E 115 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: E 198 ARG cc_start: 0.7448 (mtt-85) cc_final: 0.7181 (mtp85) REVERT: E 276 GLU cc_start: 0.5407 (tp30) cc_final: 0.5199 (tp30) REVERT: E 312 LEU cc_start: 0.6783 (mt) cc_final: 0.6576 (mt) outliers start: 22 outliers final: 11 residues processed: 184 average time/residue: 0.7109 time to fit residues: 140.5414 Evaluate side-chains 188 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 194 LEU 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 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 140 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 21 optimal weight: 0.0060 chunk 99 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.186103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146727 restraints weight = 15542.542| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.43 r_work: 0.3400 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15645 Z= 0.107 Angle : 0.587 12.356 21374 Z= 0.283 Chirality : 0.039 0.246 2457 Planarity : 0.005 0.064 2607 Dihedral : 16.414 170.079 2558 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.36 % Allowed : 16.59 % Favored : 82.05 % 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: 1.31 (0.20), residues: 1791 helix: 1.58 (0.17), residues: 951 sheet: 0.03 (0.35), residues: 227 loop : 0.21 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 228 TYR 0.008 0.001 TYR C 111 PHE 0.009 0.001 PHE A 44 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15645) covalent geometry : angle 0.58651 / 0.28 (21374) hydrogen bonds : bond 0.03232 / 2.17 ( 733) hydrogen bonds : angle 3.95434 / 2.78 ( 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 194 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.425 Fit side-chains REVERT: D 230 ARG cc_start: 0.8299 (tpp-160) cc_final: 0.7975 (tpp-160) REVERT: C 216 ASP cc_start: 0.8243 (m-30) cc_final: 0.8019 (m-30) REVERT: C 280 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8833 (t) REVERT: B 65 ASN cc_start: 0.8381 (m110) cc_final: 0.8091 (m-40) REVERT: B 92 ASP cc_start: 0.8283 (p0) cc_final: 0.7894 (m-30) REVERT: B 191 GLU cc_start: 0.8263 (mp0) cc_final: 0.7773 (mp0) REVERT: A 147 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7935 (mtp85) REVERT: A 312 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7533 (mp) REVERT: F 199 ARG cc_start: 0.8326 (mpt90) cc_final: 0.7870 (mmt-90) REVERT: F 248 ARG cc_start: 0.7441 (mtt90) cc_final: 0.6963 (mmm160) REVERT: E 115 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: E 198 ARG cc_start: 0.7600 (mtt-85) cc_final: 0.7357 (mtp85) REVERT: E 312 LEU cc_start: 0.6866 (mt) cc_final: 0.6660 (mt) outliers start: 20 outliers final: 13 residues processed: 185 average time/residue: 0.7211 time to fit residues: 143.6973 Evaluate side-chains 186 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 194 LEU 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 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 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 150 optimal weight: 0.0050 chunk 103 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.186134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146829 restraints weight = 15423.811| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.46 r_work: 0.3432 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15645 Z= 0.117 Angle : 0.598 12.706 21374 Z= 0.286 Chirality : 0.039 0.249 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.431 170.632 2558 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.22 % Allowed : 16.72 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1791 helix: 1.58 (0.17), residues: 951 sheet: 0.03 (0.35), residues: 227 loop : 0.19 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 228 TYR 0.010 0.001 TYR C 111 PHE 0.009 0.001 PHE A 44 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15645) covalent geometry : angle 0.59796 / 0.29 (21374) hydrogen bonds : bond 0.03308 / 2.24 ( 733) hydrogen bonds : angle 3.94929 / 2.78 ( 2056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.56 seconds wall clock time: 80 minutes 34.62 seconds (4834.62 seconds total)