Starting phenix.real_space_refine on Fri Jul 3 07:37:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7upr_26674/07_2026/7upr_26674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upr_26674/07_2026/7upr_26674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2026/7upr_26674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2026/7upr_26674.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2026/7upr_26674.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2026/7upr_26674.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2026/7upr_26674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2026/7upr_26674.map" } resolution = 3.2 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= 0.067 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 15 5.49 5 Mg 4 5.21 5 S 79 5.16 5 C 7976 2.51 5 N 2286 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12780 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2350 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 285} Chain breaks: 1 Chain: "B" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2181 Classifications: {'peptide': 277} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 264} Chain breaks: 2 Chain: "E" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2364 Classifications: {'peptide': 300} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 287} Chain breaks: 1 Chain: "D" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2357 Classifications: {'peptide': 299} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 286} Chain breaks: 1 Chain: "F" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2119 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 12, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1200 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 673 Unresolved non-hydrogen angles: 849 Unresolved non-hydrogen dihedrals: 556 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'HIS:plan': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 8, 'GLU:plan': 9, 'ASN:plan1': 7, 'ARG:plan': 10, 'GLN:plan1': 13, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 323 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.05, per 1000 atoms: 0.24 Number of scatterers: 12780 At special positions: 0 Unit cell: (75.712, 133.12, 137.28, 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 79 16.00 P 15 15.00 Mg 4 11.99 O 2420 8.00 N 2286 7.00 C 7976 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: 1.06 Conformation dependent library (CDL) restraints added in 592.5 milliseconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 7 sheets defined 54.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.797A pdb=" N MET C 86 " --> pdb=" O PRO C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.630A pdb=" N ILE C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.644A pdb=" N PHE C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 169 through 184 removed outlier: 3.809A pdb=" N PHE C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 removed outlier: 3.599A pdb=" N MET C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP C 221 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 4.025A pdb=" N ASP C 242 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 243 " --> pdb=" O PRO C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 239 through 243' Processing helix chain 'C' and resid 245 through 251 removed outlier: 4.080A pdb=" N ARG C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 273 Processing helix chain 'C' and resid 283 through 292 removed outlier: 3.971A pdb=" N VAL C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 316 Processing helix chain 'C' and resid 333 through 347 removed outlier: 3.801A pdb=" N HIS C 337 " --> pdb=" O GLN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'B' and resid 58 through 63 removed outlier: 4.371A pdb=" N ILE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 63' Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.510A pdb=" N ALA B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.507A pdb=" N ASN B 85 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 86 " --> pdb=" O PRO B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 86' Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.790A pdb=" N ILE B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 170 through 184 removed outlier: 3.837A pdb=" N PHE B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.610A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 261 through 273 removed outlier: 3.598A pdb=" N GLU B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.697A pdb=" N VAL B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.053A pdb=" N GLU B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR B 314 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 3.646A pdb=" N LEU B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'E' and resid 46 through 63 removed outlier: 3.737A pdb=" N ALA E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU E 56 " --> pdb=" O GLN E 52 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 97 through 107 Processing helix chain 'E' and resid 107 through 112 removed outlier: 3.664A pdb=" N ILE E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 107 through 112' Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'E' and resid 169 through 184 removed outlier: 3.743A pdb=" N PHE E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.081A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 removed outlier: 3.585A pdb=" N MET E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP E 221 " --> pdb=" O MET E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.646A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 283 through 292 removed outlier: 3.813A pdb=" N VAL E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 316 Processing helix chain 'E' and resid 334 through 350 removed outlier: 3.556A pdb=" N ARG E 338 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.663A pdb=" N GLU D 50 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 51 " --> pdb=" O LYS D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 51' Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.567A pdb=" N GLN D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.787A pdb=" N MET D 86 " --> pdb=" O PRO D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.743A pdb=" N ILE D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 112' Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.534A pdb=" N PHE D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.694A pdb=" N ALA D 150 " --> pdb=" O THR D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 184 removed outlier: 3.752A pdb=" N PHE D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.220A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 193 through 198' Processing helix chain 'D' and resid 206 through 221 removed outlier: 3.598A pdb=" N MET D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP D 221 " --> pdb=" O MET D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 3.643A pdb=" N ARG D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 Processing helix chain 'D' and resid 283 through 292 removed outlier: 4.398A pdb=" N VAL D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 317 removed outlier: 3.511A pdb=" N LEU D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 348 removed outlier: 4.088A pdb=" N HIS D 337 " --> pdb=" O GLN D 333 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 77 Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' Processing helix chain 'F' and resid 97 through 112 removed outlier: 3.661A pdb=" N ASP F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.559A pdb=" N ILE F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA F 143 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 184 removed outlier: 3.808A pdb=" N LEU F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.791A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 221 removed outlier: 3.699A pdb=" N MET F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP F 221 " --> pdb=" O MET F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'F' and resid 295 through 313 removed outlier: 3.823A pdb=" N ARG F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 317 Processing helix chain 'F' and resid 332 through 347 removed outlier: 3.697A pdb=" N LEU F 336 " --> pdb=" O GLN F 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.839A pdb=" N ALA A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.756A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.766A pdb=" N GLU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 316 removed outlier: 3.507A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 Processing sheet with id=AA1, first strand: chain 'C' and resid 153 through 156 removed outlier: 7.396A pdb=" N ARG C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N PHE C 190 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER C 187 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N MET C 234 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE C 189 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA C 236 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 129 " --> pdb=" O GLY C 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 156 removed outlier: 7.103A pdb=" N ARG B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE B 190 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER B 187 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET B 234 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE B 189 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA B 236 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 191 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 129 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR B 237 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 131 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 153 through 156 removed outlier: 7.363A pdb=" N ARG E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE E 190 " --> pdb=" O ARG E 153 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER E 187 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N MET E 234 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE E 189 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA E 236 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 129 " --> pdb=" O GLY E 235 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR E 237 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU E 131 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 153 through 156 removed outlier: 7.431A pdb=" N ARG D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE D 190 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER D 187 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET D 234 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE D 189 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA D 236 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL D 129 " --> pdb=" O GLY D 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 155 through 156 removed outlier: 6.459A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE F 189 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA F 236 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE F 191 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 237 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU F 130 " --> pdb=" O PHE F 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.834A pdb=" N PHE A 255 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 132 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 156 removed outlier: 6.357A pdb=" N ARG A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE A 190 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER A 187 " --> pdb=" O ILE A 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 520 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4305 1.35 - 1.46: 2526 1.46 - 1.58: 5976 1.58 - 1.70: 25 1.70 - 1.81: 133 Bond restraints: 12965 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.17e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.11e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.09e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.98e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.83e+01 ... (remaining 12960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 17459 3.98 - 7.97: 66 7.97 - 11.95: 15 11.95 - 15.94: 0 15.94 - 19.92: 10 Bond angle restraints: 17550 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 ... (remaining 17545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7127 17.80 - 35.60: 625 35.60 - 53.41: 161 53.41 - 71.21: 34 71.21 - 89.01: 20 Dihedral angle restraints: 7967 sinusoidal: 3037 harmonic: 4930 Sorted by residual: dihedral pdb=" CA GLU D 50 " pdb=" C GLU D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA CYS B 137 " pdb=" C CYS B 137 " pdb=" N GLY B 138 " pdb=" CA GLY B 138 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA GLN F 158 " pdb=" C GLN F 158 " pdb=" N PRO F 159 " pdb=" CA PRO F 159 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1376 0.031 - 0.062: 439 0.062 - 0.093: 134 0.093 - 0.125: 90 0.125 - 0.156: 6 Chirality restraints: 2045 Sorted by residual: chirality pdb=" CA PRO F 186 " pdb=" N PRO F 186 " pdb=" C PRO F 186 " pdb=" CB PRO F 186 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" C1' ATP B 501 " pdb=" C2' ATP B 501 " pdb=" N9 ATP B 501 " pdb=" O4' ATP B 501 " both_signs ideal model delta sigma weight residual False 2.41 2.56 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" C1' ATP F 501 " pdb=" C2' ATP F 501 " pdb=" N9 ATP F 501 " pdb=" O4' ATP F 501 " both_signs ideal model delta sigma weight residual False 2.41 2.55 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2042 not shown) Planarity restraints: 2241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 158 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO F 159 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 159 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 159 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 109 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO B 110 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 259 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO F 260 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 260 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 260 " 0.015 5.00e-02 4.00e+02 ... (remaining 2238 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 175 2.63 - 3.20: 11329 3.20 - 3.76: 19987 3.76 - 4.33: 25410 4.33 - 4.90: 42409 Nonbonded interactions: 99310 Sorted by model distance: nonbonded pdb=" O2B ATP B 501 " pdb="MG MG B 502 " model vdw 2.062 2.170 nonbonded pdb=" O2B ATP E 501 " pdb="MG MG E 502 " model vdw 2.067 2.170 nonbonded pdb=" O2B ATP D 501 " pdb="MG MG D 502 " model vdw 2.069 2.170 nonbonded pdb=" O2B ATP C 501 " pdb="MG MG C 502 " model vdw 2.093 2.170 nonbonded pdb=" O3G ATP B 501 " pdb="MG MG B 502 " model vdw 2.132 2.170 ... (remaining 99305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'F' and ((resid 86 through 94 and (name N or name CA or name C or name O \ or name CB )) or resid 95 or (resid 96 through 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 or (resid 129 through 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 or (resid 134 through 1 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 136 or (res \ id 137 and (name N or name CA or name C or name O or name CB )) or resid 138 or \ (resid 139 through 150 and (name N or name CA or name C or name O or name CB )) \ or resid 151 or (resid 152 through 161 and (name N or name CA or name C or name \ O or name CB )) or (resid 169 through 197 and (name N or name CA or name C or na \ me O or name CB )) or (resid 208 through 221 and (name N or name CA or name C or \ name O or name CB )) or resid 222 or (resid 223 through 234 and (name N or name \ CA or name C or name O or name CB )) or (resid 235 through 258 and (name N or n \ ame CA or name C or name O or name CB )) or resid 259 or (resid 260 through 292 \ and (name N or name CA or name C or name O or name CB )) or resid 293 or (resid \ 294 through 295 and (name N or name CA or name C or name O or name CB )) or resi \ d 296 or (resid 297 through 298 and (name N or name CA or name C or name O or na \ me CB )) or resid 299 through 301 or (resid 302 through 303 and (name N or name \ CA or name C or name O or name CB )) or resid 304 or (resid 305 through 307 and \ (name N or name CA or name C or name O or name CB )) or resid 308 through 309 or \ (resid 310 through 311 and (name N or name CA or name C or name O or name CB )) \ or resid 312 or (resid 313 through 314 and (name N or name CA or name C or name \ O or name CB )) or resid 315 or (resid 316 through 347 and (name N or name CA o \ r name C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 55 through 199 or resid 210 through 502)) selection = (chain 'D' and (resid 55 through 199 or resid 210 through 502)) selection = (chain 'E' and (resid 55 through 199 or resid 210 through 317 or resid 328 throu \ gh 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.910 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.004 0.085 12965 Z= 0.313 Angle : 0.796 19.923 17550 Z= 0.616 Chirality : 0.039 0.156 2045 Planarity : 0.003 0.048 2241 Dihedral : 15.491 89.009 4729 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.18 % Allowed : 14.81 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -3.02 (0.18), residues: 1648 helix: -1.14 (0.16), residues: 771 sheet: -2.78 (0.37), residues: 132 loop : -2.79 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 153 TYR 0.004 0.000 TYR D 132 PHE 0.005 0.001 PHE B 216 TRP 0.004 0.000 TRP F 90 HIS 0.003 0.000 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.31 (12965) covalent geometry : angle 0.79579 / 0.62 (17550) hydrogen bonds : bond 0.15788 / 10.26 ( 520) hydrogen bonds : angle 5.01947 / 3.39 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6893 (pp) REVERT: C 279 ASP cc_start: 0.8334 (t70) cc_final: 0.8006 (t70) REVERT: B 68 LYS cc_start: 0.8695 (mppt) cc_final: 0.8461 (mppt) REVERT: B 74 MET cc_start: 0.8259 (mtt) cc_final: 0.7947 (mtt) REVERT: B 184 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8005 (pp) REVERT: B 341 GLU cc_start: 0.8286 (tp30) cc_final: 0.7941 (mm-30) REVERT: E 45 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6130 (ttm-80) REVERT: E 60 LYS cc_start: 0.9128 (tptm) cc_final: 0.8927 (ttpt) REVERT: D 305 ASP cc_start: 0.8209 (t0) cc_final: 0.7754 (t0) REVERT: F 98 ASP cc_start: 0.7944 (t0) cc_final: 0.7559 (t0) REVERT: F 102 ASP cc_start: 0.7456 (m-30) cc_final: 0.7183 (m-30) REVERT: F 131 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7031 (mp) REVERT: F 290 GLU cc_start: 0.7947 (mp0) cc_final: 0.7665 (mp0) REVERT: F 345 LYS cc_start: 0.8395 (mmtm) cc_final: 0.8174 (pptt) REVERT: A 309 LEU cc_start: 0.8131 (mp) cc_final: 0.7865 (mp) outliers start: 53 outliers final: 35 residues processed: 330 average time/residue: 0.1105 time to fit residues: 52.2943 Evaluate side-chains 231 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 278 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS E 52 GLN E 119 ASN E 193 GLN E 264 GLN E 332 GLN D 61 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.126849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093650 restraints weight = 21650.758| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.36 r_work: 0.3177 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12965 Z= 0.129 Angle : 0.561 10.274 17550 Z= 0.281 Chirality : 0.041 0.144 2045 Planarity : 0.003 0.045 2241 Dihedral : 7.261 79.391 1855 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.65 % Allowed : 19.31 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -1.63 (0.20), residues: 1648 helix: 0.03 (0.18), residues: 802 sheet: -2.33 (0.35), residues: 159 loop : -2.08 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 250 TYR 0.026 0.001 TYR B 132 PHE 0.012 0.001 PHE B 351 TRP 0.005 0.001 TRP F 90 HIS 0.006 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (12965) covalent geometry : angle 0.56148 / 0.28 (17550) hydrogen bonds : bond 0.03509 / 2.29 ( 520) hydrogen bonds : angle 3.83920 / 2.61 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7188 (pp) REVERT: C 121 ARG cc_start: 0.8674 (tpt90) cc_final: 0.8297 (tpp80) REVERT: C 279 ASP cc_start: 0.8426 (t70) cc_final: 0.8049 (t70) REVERT: C 280 ARG cc_start: 0.8945 (tmm-80) cc_final: 0.8724 (tmm-80) REVERT: B 68 LYS cc_start: 0.8820 (mppt) cc_final: 0.8619 (mptt) REVERT: B 74 MET cc_start: 0.8366 (mtt) cc_final: 0.8002 (mtt) REVERT: B 79 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7642 (t-90) REVERT: B 184 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8005 (pp) REVERT: B 195 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: B 341 GLU cc_start: 0.8491 (tp30) cc_final: 0.7979 (mm-30) REVERT: E 45 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5124 (ttm-80) REVERT: E 74 MET cc_start: 0.8290 (tpp) cc_final: 0.7736 (mpp) REVERT: E 292 ASP cc_start: 0.8005 (t70) cc_final: 0.7744 (t0) REVERT: D 290 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7977 (mm-30) REVERT: D 305 ASP cc_start: 0.8473 (t0) cc_final: 0.7987 (t0) REVERT: F 98 ASP cc_start: 0.7913 (t0) cc_final: 0.7568 (t0) REVERT: F 102 ASP cc_start: 0.7869 (m-30) cc_final: 0.7442 (m-30) REVERT: F 345 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8211 (pptt) outliers start: 59 outliers final: 37 residues processed: 264 average time/residue: 0.1122 time to fit residues: 42.7327 Evaluate side-chains 230 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 141 optimal weight: 0.0000 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.0870 chunk 79 optimal weight: 5.9990 overall best weight: 1.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 238 ASN B 256 HIS B 259 GLN B 281 HIS E 47 GLN E 79 HIS E 119 ASN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.121826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.088152 restraints weight = 22051.474| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.37 r_work: 0.3083 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12965 Z= 0.162 Angle : 0.582 10.845 17550 Z= 0.289 Chirality : 0.042 0.158 2045 Planarity : 0.003 0.051 2241 Dihedral : 6.686 67.528 1838 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 5.04 % Allowed : 20.49 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.87 (0.21), residues: 1648 helix: 0.56 (0.19), residues: 814 sheet: -1.72 (0.45), residues: 122 loop : -1.72 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 45 TYR 0.021 0.001 TYR B 132 PHE 0.010 0.001 PHE D 154 TRP 0.006 0.001 TRP B 90 HIS 0.008 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (12965) covalent geometry : angle 0.58164 / 0.29 (17550) hydrogen bonds : bond 0.03335 / 2.20 ( 520) hydrogen bonds : angle 3.71791 / 2.57 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8639 (tpt90) cc_final: 0.8261 (tpp80) REVERT: C 279 ASP cc_start: 0.8351 (t70) cc_final: 0.7984 (t70) REVERT: C 280 ARG cc_start: 0.9096 (tmm-80) cc_final: 0.8566 (tmm-80) REVERT: C 281 HIS cc_start: 0.8086 (p-80) cc_final: 0.7551 (p-80) REVERT: B 68 LYS cc_start: 0.8850 (mppt) cc_final: 0.8554 (mppt) REVERT: B 74 MET cc_start: 0.8414 (mtt) cc_final: 0.8006 (mtt) REVERT: B 79 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7739 (t-90) REVERT: B 195 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: B 341 GLU cc_start: 0.8481 (tp30) cc_final: 0.8268 (tp30) REVERT: E 45 ARG cc_start: 0.5613 (OUTLIER) cc_final: 0.4860 (ttm-80) REVERT: E 69 LEU cc_start: 0.8612 (mp) cc_final: 0.8310 (mt) REVERT: E 74 MET cc_start: 0.8280 (tpp) cc_final: 0.7788 (mpp) REVERT: E 292 ASP cc_start: 0.8088 (t70) cc_final: 0.7771 (t0) REVERT: D 96 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7755 (pp) REVERT: D 225 THR cc_start: 0.8629 (t) cc_final: 0.8309 (p) REVERT: D 248 MET cc_start: 0.8608 (mmm) cc_final: 0.8040 (mmm) REVERT: D 290 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7992 (mm-30) REVERT: D 305 ASP cc_start: 0.8471 (t0) cc_final: 0.7944 (t0) REVERT: F 98 ASP cc_start: 0.7884 (t0) cc_final: 0.7443 (t0) REVERT: F 102 ASP cc_start: 0.7811 (m-30) cc_final: 0.7300 (m-30) REVERT: F 211 MET cc_start: 0.7837 (tmm) cc_final: 0.7633 (tmm) REVERT: F 337 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7580 (t-170) REVERT: F 345 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8156 (pptt) outliers start: 64 outliers final: 39 residues processed: 252 average time/residue: 0.1104 time to fit residues: 40.0343 Evaluate side-chains 226 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 337 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 0.5980 chunk 63 optimal weight: 0.0270 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 79 HIS E 119 ASN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.089636 restraints weight = 21820.253| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.36 r_work: 0.3105 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12965 Z= 0.112 Angle : 0.549 10.783 17550 Z= 0.270 Chirality : 0.040 0.167 2045 Planarity : 0.003 0.042 2241 Dihedral : 6.410 65.179 1831 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.89 % Allowed : 21.12 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.50 (0.22), residues: 1648 helix: 0.87 (0.20), residues: 813 sheet: -1.61 (0.42), residues: 141 loop : -1.49 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 45 TYR 0.018 0.001 TYR B 132 PHE 0.009 0.001 PHE B 154 TRP 0.004 0.001 TRP F 90 HIS 0.003 0.000 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (12965) covalent geometry : angle 0.54885 / 0.27 (17550) hydrogen bonds : bond 0.02923 / 1.92 ( 520) hydrogen bonds : angle 3.58922 / 2.49 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8619 (tpt90) cc_final: 0.8255 (tpp80) REVERT: C 279 ASP cc_start: 0.8346 (t70) cc_final: 0.8010 (t70) REVERT: C 280 ARG cc_start: 0.9051 (tmm-80) cc_final: 0.8550 (tmm-80) REVERT: C 281 HIS cc_start: 0.8005 (p-80) cc_final: 0.7372 (p-80) REVERT: B 68 LYS cc_start: 0.8843 (mppt) cc_final: 0.8554 (mptt) REVERT: B 74 MET cc_start: 0.8486 (mtt) cc_final: 0.8084 (mtt) REVERT: B 79 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7791 (t-90) REVERT: B 195 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: B 341 GLU cc_start: 0.8499 (tp30) cc_final: 0.7995 (mm-30) REVERT: E 74 MET cc_start: 0.8334 (tpp) cc_final: 0.7843 (mpp) REVERT: E 292 ASP cc_start: 0.8062 (t70) cc_final: 0.7773 (t0) REVERT: E 312 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7312 (ttm-80) REVERT: D 225 THR cc_start: 0.8725 (t) cc_final: 0.8426 (p) REVERT: D 248 MET cc_start: 0.8599 (mmm) cc_final: 0.8003 (mmm) REVERT: D 290 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7953 (mm-30) REVERT: D 305 ASP cc_start: 0.8493 (t0) cc_final: 0.7979 (t0) REVERT: F 98 ASP cc_start: 0.7944 (t0) cc_final: 0.7451 (t0) REVERT: F 102 ASP cc_start: 0.7882 (m-30) cc_final: 0.7320 (m-30) REVERT: F 211 MET cc_start: 0.7775 (tmm) cc_final: 0.7458 (tmm) REVERT: F 275 ASN cc_start: 0.7717 (p0) cc_final: 0.7513 (p0) REVERT: F 345 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8164 (pptt) outliers start: 62 outliers final: 39 residues processed: 249 average time/residue: 0.0956 time to fit residues: 35.0827 Evaluate side-chains 229 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 61 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 86 optimal weight: 0.0170 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 238 ASN E 79 HIS E 119 ASN E 206 HIS E 337 HIS D 79 HIS D 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089808 restraints weight = 21682.739| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.35 r_work: 0.3112 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12965 Z= 0.105 Angle : 0.548 11.421 17550 Z= 0.268 Chirality : 0.040 0.181 2045 Planarity : 0.003 0.041 2241 Dihedral : 6.116 62.949 1822 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.57 % Allowed : 21.36 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.29 (0.22), residues: 1648 helix: 1.07 (0.20), residues: 813 sheet: -1.47 (0.40), residues: 154 loop : -1.42 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 312 TYR 0.006 0.001 TYR F 132 PHE 0.014 0.001 PHE E 117 TRP 0.004 0.001 TRP E 220 HIS 0.004 0.000 HIS F 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (12965) covalent geometry : angle 0.54810 / 0.27 (17550) hydrogen bonds : bond 0.02796 / 1.83 ( 520) hydrogen bonds : angle 3.53292 / 2.46 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8657 (tm-30) REVERT: C 121 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8280 (tpp80) REVERT: C 279 ASP cc_start: 0.8356 (t70) cc_final: 0.8140 (t70) REVERT: C 280 ARG cc_start: 0.9019 (tmm-80) cc_final: 0.8750 (mmm160) REVERT: B 68 LYS cc_start: 0.8853 (mppt) cc_final: 0.8557 (mptt) REVERT: B 74 MET cc_start: 0.8476 (mtt) cc_final: 0.8078 (mtt) REVERT: B 341 GLU cc_start: 0.8508 (tp30) cc_final: 0.8005 (mm-30) REVERT: E 74 MET cc_start: 0.8290 (tpp) cc_final: 0.7847 (mpp) REVERT: E 187 SER cc_start: 0.9418 (p) cc_final: 0.8972 (m) REVERT: E 292 ASP cc_start: 0.8087 (t70) cc_final: 0.7780 (t0) REVERT: E 312 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7313 (ttm-80) REVERT: D 225 THR cc_start: 0.8749 (t) cc_final: 0.8416 (p) REVERT: D 248 MET cc_start: 0.8599 (mmm) cc_final: 0.8048 (mmm) REVERT: D 290 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7966 (mm-30) REVERT: D 305 ASP cc_start: 0.8481 (t0) cc_final: 0.7976 (t0) REVERT: F 98 ASP cc_start: 0.7958 (t0) cc_final: 0.7426 (t0) REVERT: F 102 ASP cc_start: 0.7887 (m-30) cc_final: 0.7287 (m-30) REVERT: F 211 MET cc_start: 0.7785 (tmm) cc_final: 0.7431 (tmm) REVERT: F 275 ASN cc_start: 0.7693 (p0) cc_final: 0.7425 (p0) REVERT: F 345 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8157 (pptt) outliers start: 58 outliers final: 40 residues processed: 250 average time/residue: 0.0964 time to fit residues: 35.5729 Evaluate side-chains 228 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 154 optimal weight: 50.0000 chunk 9 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 238 ASN B 281 HIS E 79 HIS E 119 ASN E 337 HIS D 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.089417 restraints weight = 21414.910| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.33 r_work: 0.3107 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12965 Z= 0.110 Angle : 0.560 11.300 17550 Z= 0.271 Chirality : 0.040 0.214 2045 Planarity : 0.003 0.040 2241 Dihedral : 6.093 61.025 1819 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.57 % Allowed : 22.06 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.16 (0.22), residues: 1648 helix: 1.17 (0.20), residues: 815 sheet: -1.24 (0.41), residues: 153 loop : -1.41 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 280 TYR 0.006 0.001 TYR F 132 PHE 0.008 0.001 PHE B 154 TRP 0.004 0.001 TRP E 220 HIS 0.006 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12965) covalent geometry : angle 0.55963 / 0.27 (17550) hydrogen bonds : bond 0.02780 / 1.82 ( 520) hydrogen bonds : angle 3.51286 / 2.45 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8694 (tm-30) REVERT: C 121 ARG cc_start: 0.8646 (tpt90) cc_final: 0.8290 (tpp80) REVERT: C 279 ASP cc_start: 0.8483 (t70) cc_final: 0.8164 (t70) REVERT: B 68 LYS cc_start: 0.8874 (mppt) cc_final: 0.8566 (mptt) REVERT: B 74 MET cc_start: 0.8469 (mtt) cc_final: 0.8066 (mtt) REVERT: B 257 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8414 (mm) REVERT: B 281 HIS cc_start: 0.8317 (p90) cc_final: 0.8104 (p90) REVERT: B 341 GLU cc_start: 0.8497 (tp30) cc_final: 0.7999 (mm-30) REVERT: E 74 MET cc_start: 0.8294 (tpp) cc_final: 0.7862 (mpp) REVERT: E 292 ASP cc_start: 0.8045 (t70) cc_final: 0.7767 (t0) REVERT: E 312 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7228 (ttm-80) REVERT: D 118 GLU cc_start: 0.8565 (pp20) cc_final: 0.8117 (pm20) REVERT: D 225 THR cc_start: 0.8764 (t) cc_final: 0.8452 (p) REVERT: D 248 MET cc_start: 0.8579 (mmm) cc_final: 0.8029 (mmm) REVERT: D 290 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7971 (mm-30) REVERT: D 305 ASP cc_start: 0.8477 (t0) cc_final: 0.7969 (t0) REVERT: F 98 ASP cc_start: 0.7921 (t0) cc_final: 0.7359 (t0) REVERT: F 102 ASP cc_start: 0.7910 (m-30) cc_final: 0.7285 (m-30) REVERT: F 207 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6115 (pp20) REVERT: F 275 ASN cc_start: 0.7733 (p0) cc_final: 0.7434 (p0) REVERT: F 345 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8150 (pptt) outliers start: 58 outliers final: 48 residues processed: 241 average time/residue: 0.0994 time to fit residues: 34.8060 Evaluate side-chains 235 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 79 HIS E 119 ASN E 337 HIS D 79 HIS F 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.122387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089195 restraints weight = 21559.259| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.35 r_work: 0.3104 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12965 Z= 0.114 Angle : 0.560 11.028 17550 Z= 0.273 Chirality : 0.040 0.215 2045 Planarity : 0.003 0.039 2241 Dihedral : 6.084 59.586 1817 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 4.41 % Allowed : 22.77 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.12 (0.22), residues: 1648 helix: 1.18 (0.20), residues: 822 sheet: -1.09 (0.41), residues: 152 loop : -1.43 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 239 TYR 0.006 0.001 TYR F 132 PHE 0.010 0.001 PHE B 351 TRP 0.004 0.001 TRP F 90 HIS 0.005 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (12965) covalent geometry : angle 0.56032 / 0.27 (17550) hydrogen bonds : bond 0.02746 / 1.80 ( 520) hydrogen bonds : angle 3.48506 / 2.43 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8653 (tpt90) cc_final: 0.8300 (tpp80) REVERT: C 279 ASP cc_start: 0.8497 (t70) cc_final: 0.8175 (t70) REVERT: B 68 LYS cc_start: 0.8871 (mppt) cc_final: 0.8577 (mptt) REVERT: B 74 MET cc_start: 0.8469 (mtt) cc_final: 0.8058 (mtt) REVERT: B 257 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8412 (mm) REVERT: B 281 HIS cc_start: 0.8347 (p90) cc_final: 0.8144 (p90) REVERT: B 341 GLU cc_start: 0.8507 (tp30) cc_final: 0.8007 (mm-30) REVERT: E 74 MET cc_start: 0.8300 (tpp) cc_final: 0.7859 (mpp) REVERT: E 292 ASP cc_start: 0.8050 (t70) cc_final: 0.7776 (t0) REVERT: E 312 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7315 (ttm-80) REVERT: D 118 GLU cc_start: 0.8562 (pp20) cc_final: 0.8133 (pm20) REVERT: D 225 THR cc_start: 0.8791 (t) cc_final: 0.8457 (p) REVERT: D 248 MET cc_start: 0.8577 (mmm) cc_final: 0.8021 (mmm) REVERT: D 290 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7992 (mm-30) REVERT: D 305 ASP cc_start: 0.8490 (t0) cc_final: 0.7979 (t0) REVERT: F 102 ASP cc_start: 0.7927 (m-30) cc_final: 0.7284 (m-30) REVERT: F 158 GLN cc_start: 0.5882 (tp40) cc_final: 0.5565 (mm-40) REVERT: F 207 GLU cc_start: 0.6395 (mm-30) cc_final: 0.6144 (pp20) REVERT: F 275 ASN cc_start: 0.7660 (p0) cc_final: 0.7353 (p0) REVERT: F 345 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8149 (pptt) outliers start: 56 outliers final: 47 residues processed: 233 average time/residue: 0.0949 time to fit residues: 32.6038 Evaluate side-chains 234 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 147 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 GLN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 79 HIS E 119 ASN E 337 HIS D 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.118016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084581 restraints weight = 21686.779| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.32 r_work: 0.3019 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12965 Z= 0.178 Angle : 0.609 10.115 17550 Z= 0.300 Chirality : 0.043 0.216 2045 Planarity : 0.004 0.041 2241 Dihedral : 6.461 59.558 1817 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.04 % Allowed : 22.14 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.11 (0.22), residues: 1648 helix: 1.17 (0.20), residues: 814 sheet: -1.08 (0.41), residues: 154 loop : -1.36 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 199 TYR 0.007 0.001 TYR D 167 PHE 0.011 0.002 PHE E 154 TRP 0.008 0.001 TRP E 220 HIS 0.022 0.001 HIS F 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (12965) covalent geometry : angle 0.60896 / 0.30 (17550) hydrogen bonds : bond 0.03212 / 2.12 ( 520) hydrogen bonds : angle 3.61083 / 2.53 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: C 121 ARG cc_start: 0.8684 (tpt90) cc_final: 0.8305 (tpp80) REVERT: C 279 ASP cc_start: 0.8414 (t70) cc_final: 0.8102 (t70) REVERT: B 68 LYS cc_start: 0.8855 (mppt) cc_final: 0.8568 (mptt) REVERT: B 74 MET cc_start: 0.8494 (mtt) cc_final: 0.8058 (mtt) REVERT: B 257 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8382 (mm) REVERT: B 341 GLU cc_start: 0.8537 (tp30) cc_final: 0.8304 (tp30) REVERT: E 45 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5066 (ttm-80) REVERT: E 74 MET cc_start: 0.8348 (tpp) cc_final: 0.7856 (mpp) REVERT: E 199 ARG cc_start: 0.8723 (ttp80) cc_final: 0.8239 (ttm-80) REVERT: E 292 ASP cc_start: 0.8122 (t70) cc_final: 0.7813 (t0) REVERT: E 312 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7508 (ttm-80) REVERT: D 118 GLU cc_start: 0.8612 (pp20) cc_final: 0.8200 (pm20) REVERT: D 225 THR cc_start: 0.8821 (t) cc_final: 0.8504 (p) REVERT: D 290 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8130 (mm-30) REVERT: F 102 ASP cc_start: 0.7864 (m-30) cc_final: 0.7643 (m-30) REVERT: F 275 ASN cc_start: 0.7585 (p0) cc_final: 0.7309 (p0) REVERT: F 345 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8114 (pptt) outliers start: 64 outliers final: 50 residues processed: 235 average time/residue: 0.0952 time to fit residues: 32.6102 Evaluate side-chains 233 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 119 ASN E 337 HIS D 79 HIS F 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.119731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086538 restraints weight = 21743.191| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.34 r_work: 0.3052 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12965 Z= 0.121 Angle : 0.586 10.643 17550 Z= 0.286 Chirality : 0.041 0.204 2045 Planarity : 0.003 0.039 2241 Dihedral : 6.325 59.701 1817 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.26 % Allowed : 22.77 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.05 (0.22), residues: 1648 helix: 1.26 (0.20), residues: 822 sheet: -0.97 (0.41), residues: 154 loop : -1.26 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 280 TYR 0.006 0.001 TYR F 132 PHE 0.011 0.001 PHE B 351 TRP 0.006 0.001 TRP C 90 HIS 0.005 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (12965) covalent geometry : angle 0.58598 / 0.29 (17550) hydrogen bonds : bond 0.02899 / 1.92 ( 520) hydrogen bonds : angle 3.53897 / 2.48 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8682 (tpt90) cc_final: 0.8308 (tpp80) REVERT: C 279 ASP cc_start: 0.8517 (t70) cc_final: 0.8171 (t70) REVERT: B 68 LYS cc_start: 0.8847 (mppt) cc_final: 0.8555 (mptt) REVERT: B 74 MET cc_start: 0.8470 (mtt) cc_final: 0.8046 (mtt) REVERT: B 257 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8360 (mm) REVERT: B 341 GLU cc_start: 0.8531 (tp30) cc_final: 0.8301 (tp30) REVERT: E 74 MET cc_start: 0.8326 (tpp) cc_final: 0.7842 (mpp) REVERT: E 286 GLU cc_start: 0.8873 (tp30) cc_final: 0.8445 (tt0) REVERT: E 292 ASP cc_start: 0.8099 (t70) cc_final: 0.7780 (t0) REVERT: E 312 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7550 (ttm-80) REVERT: E 337 HIS cc_start: 0.7460 (m90) cc_final: 0.7188 (m-70) REVERT: D 118 GLU cc_start: 0.8607 (pp20) cc_final: 0.8224 (pm20) REVERT: D 121 ARG cc_start: 0.9063 (tpt-90) cc_final: 0.8816 (tpp80) REVERT: D 225 THR cc_start: 0.8809 (t) cc_final: 0.8473 (p) REVERT: D 290 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8088 (mm-30) REVERT: F 74 MET cc_start: 0.8195 (tpp) cc_final: 0.7987 (mmp) REVERT: F 102 ASP cc_start: 0.7870 (m-30) cc_final: 0.7647 (m-30) REVERT: F 158 GLN cc_start: 0.6842 (mm-40) cc_final: 0.6556 (mm-40) REVERT: F 275 ASN cc_start: 0.7580 (p0) cc_final: 0.7309 (p0) REVERT: F 345 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8001 (pptt) outliers start: 54 outliers final: 45 residues processed: 234 average time/residue: 0.0965 time to fit residues: 32.8900 Evaluate side-chains 227 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 0.6980 chunk 151 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 99 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 119 ASN D 79 HIS F 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.120304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087219 restraints weight = 21657.671| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.34 r_work: 0.3063 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12965 Z= 0.117 Angle : 0.588 10.544 17550 Z= 0.286 Chirality : 0.041 0.193 2045 Planarity : 0.003 0.038 2241 Dihedral : 6.272 58.632 1817 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.94 % Allowed : 23.25 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.14 (0.22), residues: 1648 helix: 1.36 (0.20), residues: 816 sheet: -1.01 (0.41), residues: 160 loop : -1.21 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 280 TYR 0.006 0.001 TYR F 132 PHE 0.009 0.001 PHE F 154 TRP 0.005 0.001 TRP F 90 HIS 0.007 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (12965) covalent geometry : angle 0.58829 / 0.29 (17550) hydrogen bonds : bond 0.02814 / 1.86 ( 520) hydrogen bonds : angle 3.51340 / 2.46 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8688 (tpt90) cc_final: 0.8317 (tpp80) REVERT: C 224 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7551 (t0) REVERT: C 279 ASP cc_start: 0.8534 (t70) cc_final: 0.8149 (t70) REVERT: B 68 LYS cc_start: 0.8837 (mppt) cc_final: 0.8531 (mptt) REVERT: B 74 MET cc_start: 0.8475 (mtt) cc_final: 0.8057 (mtt) REVERT: B 257 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8345 (mm) REVERT: B 341 GLU cc_start: 0.8539 (tp30) cc_final: 0.8312 (tp30) REVERT: E 74 MET cc_start: 0.8307 (tpp) cc_final: 0.7817 (mpp) REVERT: E 286 GLU cc_start: 0.8888 (tp30) cc_final: 0.8475 (tt0) REVERT: E 292 ASP cc_start: 0.8080 (t70) cc_final: 0.7753 (t0) REVERT: E 312 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7254 (ttm-80) REVERT: E 337 HIS cc_start: 0.7447 (m90) cc_final: 0.7175 (m-70) REVERT: D 118 GLU cc_start: 0.8612 (pp20) cc_final: 0.8232 (pm20) REVERT: D 121 ARG cc_start: 0.9066 (tpt-90) cc_final: 0.8825 (tpp80) REVERT: D 225 THR cc_start: 0.8797 (t) cc_final: 0.8429 (p) REVERT: D 290 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8057 (mm-30) REVERT: D 305 ASP cc_start: 0.8511 (t0) cc_final: 0.8006 (t0) REVERT: F 74 MET cc_start: 0.8216 (tpp) cc_final: 0.7656 (mpp) REVERT: F 102 ASP cc_start: 0.7874 (m-30) cc_final: 0.7638 (m-30) REVERT: F 158 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6711 (mm-40) REVERT: F 275 ASN cc_start: 0.7544 (p0) cc_final: 0.7280 (p0) REVERT: F 345 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8002 (pptt) outliers start: 50 outliers final: 45 residues processed: 227 average time/residue: 0.0917 time to fit residues: 30.3738 Evaluate side-chains 225 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 154 optimal weight: 50.0000 chunk 145 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 144 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN D 79 HIS F 79 HIS F 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.120292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087020 restraints weight = 21564.349| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.34 r_work: 0.3063 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 12965 Z= 0.222 Angle : 0.839 59.155 17550 Z= 0.478 Chirality : 0.044 0.679 2045 Planarity : 0.003 0.038 2241 Dihedral : 6.244 58.591 1815 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.02 % Allowed : 23.33 % Favored : 72.66 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.04 % 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: 0.14 (0.22), residues: 1648 helix: 1.36 (0.20), residues: 816 sheet: -1.01 (0.41), residues: 160 loop : -1.21 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG D 280 TYR 0.006 0.001 TYR F 132 PHE 0.009 0.001 PHE B 117 TRP 0.005 0.001 TRP F 90 HIS 0.050 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.22 (12965) covalent geometry : angle 0.83942 / 0.48 (17550) hydrogen bonds : bond 0.02822 / 1.86 ( 520) hydrogen bonds : angle 3.51362 / 2.46 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2888.44 seconds wall clock time: 50 minutes 17.75 seconds (3017.75 seconds total)