Starting phenix.real_space_refine on Wed Mar 4 10:25:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upr_26674/03_2026/7upr_26674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upr_26674/03_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_26674/03_2026/7upr_26674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upr_26674/03_2026/7upr_26674.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upr_26674/03_2026/7upr_26674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upr_26674/03_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-5986/lib/python3.9/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: 3.23, per 1000 atoms: 0.25 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: 1.14 Conformation dependent library (CDL) restraints added in 597.0 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: 0.40 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: 1.93 Time building geometry restraints manager: 1.52 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: 7210 17.80 - 35.60: 678 35.60 - 53.41: 180 53.41 - 71.21: 34 71.21 - 89.01: 20 Dihedral angle restraints: 8122 sinusoidal: 3192 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 8119 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.870 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 15.822 89.009 4884 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 covalent geometry : bond 0.00374 (12965) covalent geometry : angle 0.79579 (17550) hydrogen bonds : bond 0.15788 ( 520) hydrogen bonds : angle 5.01947 ( 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 : 0.391 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: 0.1141 time to fit residues: 53.4306 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 : 0.528 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 79 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.126970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093804 restraints weight = 21657.693| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.35 r_work: 0.3180 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1433 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= 0.128 Angle : 0.574 10.446 17550 Z= 0.287 Chirality : 0.041 0.142 2045 Planarity : 0.003 0.044 2241 Dihedral : 10.022 81.152 2010 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.57 % Allowed : 19.15 % Favored : 76.28 % 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: -1.66 (0.20), residues: 1648 helix: 0.01 (0.18), residues: 803 sheet: -2.35 (0.35), residues: 159 loop : -2.10 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 280 TYR 0.025 0.001 TYR B 132 PHE 0.012 0.001 PHE B 351 TRP 0.006 0.001 TRP B 166 HIS 0.006 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00296 (12965) covalent geometry : angle 0.57383 (17550) hydrogen bonds : bond 0.03497 ( 520) hydrogen bonds : angle 3.83992 ( 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 272 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7179 (pp) REVERT: C 121 ARG cc_start: 0.8674 (tpt90) cc_final: 0.8316 (tpp80) REVERT: C 279 ASP cc_start: 0.8424 (t70) cc_final: 0.8039 (t70) REVERT: C 280 ARG cc_start: 0.8936 (tmm-80) cc_final: 0.8706 (tmm-80) REVERT: B 68 LYS cc_start: 0.8819 (mppt) cc_final: 0.8617 (mptt) REVERT: B 74 MET cc_start: 0.8372 (mtt) cc_final: 0.8005 (mtt) REVERT: B 79 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7627 (t-90) REVERT: B 184 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7999 (pp) REVERT: B 195 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: B 341 GLU cc_start: 0.8490 (tp30) cc_final: 0.7978 (mm-30) REVERT: E 45 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5131 (ttm-80) REVERT: E 74 MET cc_start: 0.8257 (tpp) cc_final: 0.7698 (mpp) REVERT: E 121 ARG cc_start: 0.8515 (tpp80) cc_final: 0.7951 (tpp80) REVERT: E 292 ASP cc_start: 0.8058 (t70) cc_final: 0.7804 (t0) REVERT: D 290 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7975 (mm-30) REVERT: D 305 ASP cc_start: 0.8465 (t0) cc_final: 0.7985 (t0) REVERT: F 102 ASP cc_start: 0.7874 (m-30) cc_final: 0.7470 (m-30) REVERT: F 345 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8204 (pptt) outliers start: 58 outliers final: 36 residues processed: 265 average time/residue: 0.1193 time to fit residues: 45.4032 Evaluate side-chains 229 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 90 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 141 optimal weight: 0.0170 chunk 88 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 238 ASN B 256 HIS B 259 GLN B 281 HIS E 119 ASN D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.126454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093363 restraints weight = 21757.959| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.38 r_work: 0.3165 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12965 Z= 0.112 Angle : 0.548 11.068 17550 Z= 0.270 Chirality : 0.040 0.151 2045 Planarity : 0.003 0.043 2241 Dihedral : 9.574 82.901 1993 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.33 % Allowed : 21.04 % Favored : 74.63 % 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: -0.97 (0.21), residues: 1648 helix: 0.59 (0.19), residues: 805 sheet: -1.99 (0.36), residues: 161 loop : -1.78 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 45 TYR 0.021 0.001 TYR B 132 PHE 0.009 0.001 PHE C 117 TRP 0.005 0.001 TRP B 90 HIS 0.008 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00256 (12965) covalent geometry : angle 0.54771 (17550) hydrogen bonds : bond 0.03056 ( 520) hydrogen bonds : angle 3.67021 ( 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 254 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7282 (pp) REVERT: C 121 ARG cc_start: 0.8664 (tpt90) cc_final: 0.8278 (tpp80) REVERT: C 279 ASP cc_start: 0.8405 (t70) cc_final: 0.8029 (t70) REVERT: C 280 ARG cc_start: 0.9024 (tmm-80) cc_final: 0.8524 (tmm-80) REVERT: B 68 LYS cc_start: 0.8841 (mppt) cc_final: 0.8544 (mppt) REVERT: B 74 MET cc_start: 0.8381 (mtt) cc_final: 0.8008 (mtt) REVERT: B 79 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.7725 (t-90) REVERT: B 132 TYR cc_start: 0.8559 (p90) cc_final: 0.8347 (p90) REVERT: B 195 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: B 341 GLU cc_start: 0.8484 (tp30) cc_final: 0.7977 (mm-30) REVERT: E 45 ARG cc_start: 0.5669 (OUTLIER) cc_final: 0.4921 (ttm-80) REVERT: E 74 MET cc_start: 0.8267 (tpp) cc_final: 0.7742 (mpp) REVERT: E 292 ASP cc_start: 0.8010 (t70) cc_final: 0.7727 (t0) REVERT: D 225 THR cc_start: 0.8646 (t) cc_final: 0.8323 (p) REVERT: D 290 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7915 (mm-30) REVERT: D 305 ASP cc_start: 0.8469 (t0) cc_final: 0.7976 (t0) REVERT: F 98 ASP cc_start: 0.7936 (t0) cc_final: 0.7512 (t0) REVERT: F 102 ASP cc_start: 0.7853 (m-30) cc_final: 0.7386 (m-30) REVERT: F 275 ASN cc_start: 0.7776 (p0) cc_final: 0.7563 (p0) REVERT: F 345 LYS cc_start: 0.8401 (mmtm) cc_final: 0.8199 (pptt) outliers start: 55 outliers final: 35 residues processed: 245 average time/residue: 0.1047 time to fit residues: 37.5974 Evaluate side-chains 227 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN B 281 HIS E 79 HIS E 119 ASN E 206 HIS E 277 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.124183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090768 restraints weight = 21676.669| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.37 r_work: 0.3133 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12965 Z= 0.120 Angle : 0.546 9.994 17550 Z= 0.269 Chirality : 0.041 0.163 2045 Planarity : 0.003 0.043 2241 Dihedral : 9.536 83.881 1987 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.65 % Allowed : 20.49 % Favored : 74.86 % 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: -0.58 (0.21), residues: 1648 helix: 0.87 (0.20), residues: 806 sheet: -1.58 (0.40), residues: 148 loop : -1.61 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 45 TYR 0.019 0.001 TYR B 132 PHE 0.010 0.001 PHE F 197 TRP 0.005 0.001 TRP D 166 HIS 0.010 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00279 (12965) covalent geometry : angle 0.54561 (17550) hydrogen bonds : bond 0.02938 ( 520) hydrogen bonds : angle 3.57377 ( 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 255 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8660 (tpt90) cc_final: 0.8281 (tpp80) REVERT: C 279 ASP cc_start: 0.8385 (t70) cc_final: 0.8095 (t70) REVERT: C 280 ARG cc_start: 0.8997 (tmm-80) cc_final: 0.8713 (mmm160) REVERT: B 59 MET cc_start: 0.6034 (tpt) cc_final: 0.5711 (tpt) REVERT: B 68 LYS cc_start: 0.8844 (mppt) cc_final: 0.8561 (mptt) REVERT: B 74 MET cc_start: 0.8427 (mtt) cc_final: 0.8037 (mtt) REVERT: B 79 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7761 (t-90) REVERT: B 195 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: B 341 GLU cc_start: 0.8498 (tp30) cc_final: 0.7992 (mm-30) REVERT: E 74 MET cc_start: 0.8289 (tpp) cc_final: 0.7805 (mpp) REVERT: E 280 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8044 (tmm160) REVERT: E 292 ASP cc_start: 0.8042 (t70) cc_final: 0.7752 (t0) REVERT: D 225 THR cc_start: 0.8742 (t) cc_final: 0.8430 (p) REVERT: D 290 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7962 (mm-30) REVERT: D 305 ASP cc_start: 0.8492 (t0) cc_final: 0.8003 (t0) REVERT: F 98 ASP cc_start: 0.7959 (t0) cc_final: 0.7485 (t0) REVERT: F 102 ASP cc_start: 0.7873 (m-30) cc_final: 0.7334 (m-30) REVERT: F 275 ASN cc_start: 0.7762 (p0) cc_final: 0.7522 (p0) REVERT: F 337 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7498 (t-170) REVERT: F 345 LYS cc_start: 0.8397 (mmtm) cc_final: 0.8179 (pptt) outliers start: 59 outliers final: 37 residues processed: 242 average time/residue: 0.1073 time to fit residues: 37.8566 Evaluate side-chains 228 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain B residue 79 HIS 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 238 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 47 GLN 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 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 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 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 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 337 HIS 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: 1.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 86 optimal weight: 0.0060 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 chunk 163 optimal weight: 20.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 79 HIS E 119 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS D 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.091320 restraints weight = 21646.663| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.39 r_work: 0.3142 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12965 Z= 0.105 Angle : 0.544 10.077 17550 Z= 0.265 Chirality : 0.040 0.160 2045 Planarity : 0.003 0.041 2241 Dihedral : 9.223 84.691 1975 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 4.33 % Allowed : 21.43 % Favored : 74.23 % 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: -0.35 (0.22), residues: 1648 helix: 1.07 (0.20), residues: 806 sheet: -1.38 (0.43), residues: 140 loop : -1.54 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 45 TYR 0.016 0.001 TYR B 132 PHE 0.012 0.001 PHE C 197 TRP 0.004 0.001 TRP B 90 HIS 0.003 0.000 HIS F 79 Details of bonding type rmsd covalent geometry : bond 0.00243 (12965) covalent geometry : angle 0.54435 (17550) hydrogen bonds : bond 0.02775 ( 520) hydrogen bonds : angle 3.52488 ( 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 252 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8674 (tm-30) REVERT: C 121 ARG cc_start: 0.8629 (tpt90) cc_final: 0.8269 (tpp80) REVERT: C 279 ASP cc_start: 0.8371 (t70) cc_final: 0.8064 (t70) REVERT: C 280 ARG cc_start: 0.8998 (tmm-80) cc_final: 0.8703 (mmm160) REVERT: B 59 MET cc_start: 0.6024 (tpt) cc_final: 0.5312 (tpt) REVERT: B 68 LYS cc_start: 0.8835 (mppt) cc_final: 0.8538 (mptt) REVERT: B 74 MET cc_start: 0.8407 (mtt) cc_final: 0.8011 (mtt) REVERT: B 79 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7762 (t-90) REVERT: B 341 GLU cc_start: 0.8485 (tp30) cc_final: 0.7987 (mm-30) REVERT: E 74 MET cc_start: 0.8303 (tpp) cc_final: 0.7828 (mpp) REVERT: E 292 ASP cc_start: 0.8031 (t70) cc_final: 0.7744 (t0) REVERT: D 225 THR cc_start: 0.8740 (t) cc_final: 0.8412 (p) REVERT: D 290 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7951 (mm-30) REVERT: D 305 ASP cc_start: 0.8462 (t0) cc_final: 0.7981 (t0) REVERT: F 98 ASP cc_start: 0.7951 (t0) cc_final: 0.7436 (t0) REVERT: F 102 ASP cc_start: 0.7866 (m-30) cc_final: 0.7282 (m-30) REVERT: F 275 ASN cc_start: 0.7670 (p0) cc_final: 0.7438 (p0) REVERT: F 337 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7437 (t-170) REVERT: F 345 LYS cc_start: 0.8392 (mmtm) cc_final: 0.8167 (pptt) outliers start: 55 outliers final: 39 residues processed: 242 average time/residue: 0.0996 time to fit residues: 36.0133 Evaluate side-chains 223 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 232 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 88 VAL 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 217 MET Chi-restraints excluded: chain D residue 232 ILE 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 232 ILE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 337 HIS 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: 5.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 154 optimal weight: 50.0000 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.123311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.089562 restraints weight = 21573.000| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.37 r_work: 0.3115 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12965 Z= 0.121 Angle : 0.558 9.319 17550 Z= 0.273 Chirality : 0.041 0.157 2045 Planarity : 0.003 0.041 2241 Dihedral : 9.303 85.268 1973 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.26 % Allowed : 21.36 % Favored : 74.39 % 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: 1.16 (0.20), residues: 814 sheet: -1.18 (0.42), residues: 153 loop : -1.42 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 280 TYR 0.014 0.001 TYR B 132 PHE 0.011 0.001 PHE B 351 TRP 0.004 0.001 TRP D 166 HIS 0.008 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00283 (12965) covalent geometry : angle 0.55788 (17550) hydrogen bonds : bond 0.02849 ( 520) hydrogen bonds : angle 3.51061 ( 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 240 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8703 (tm-30) REVERT: C 121 ARG cc_start: 0.8651 (tpt90) cc_final: 0.8292 (tpp80) REVERT: C 279 ASP cc_start: 0.8491 (t70) cc_final: 0.8149 (t70) REVERT: C 280 ARG cc_start: 0.9021 (tmm-80) cc_final: 0.8757 (mmm160) REVERT: B 68 LYS cc_start: 0.8882 (mppt) cc_final: 0.8588 (mptt) REVERT: B 74 MET cc_start: 0.8440 (mtt) cc_final: 0.8016 (mtt) REVERT: B 79 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.7925 (t-90) REVERT: B 341 GLU cc_start: 0.8506 (tp30) cc_final: 0.8287 (tp30) REVERT: E 74 MET cc_start: 0.8319 (tpp) cc_final: 0.7832 (mpp) REVERT: E 121 ARG cc_start: 0.8364 (tpp80) cc_final: 0.8152 (tpp80) REVERT: E 281 HIS cc_start: 0.8540 (p90) cc_final: 0.8295 (p90) REVERT: E 292 ASP cc_start: 0.8026 (t70) cc_final: 0.7755 (t0) REVERT: E 312 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7233 (ttm-80) REVERT: D 225 THR cc_start: 0.8770 (t) cc_final: 0.8447 (p) REVERT: D 290 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7940 (mm-30) REVERT: D 305 ASP cc_start: 0.8486 (t0) cc_final: 0.7984 (t0) REVERT: F 102 ASP cc_start: 0.7916 (m-30) cc_final: 0.7299 (m-30) REVERT: F 207 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6125 (pp20) REVERT: F 275 ASN cc_start: 0.7609 (p0) cc_final: 0.7394 (p0) REVERT: F 345 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8159 (pptt) outliers start: 54 outliers final: 42 residues processed: 229 average time/residue: 0.1027 time to fit residues: 34.4258 Evaluate side-chains 223 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 47 GLN 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 245 SER 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 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 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: 0.6980 chunk 95 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 GLN B 238 ASN B 281 HIS E 79 HIS E 119 ASN E 193 GLN E 238 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.119352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085872 restraints weight = 21742.978| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.34 r_work: 0.3052 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12965 Z= 0.171 Angle : 0.589 9.234 17550 Z= 0.291 Chirality : 0.042 0.189 2045 Planarity : 0.003 0.042 2241 Dihedral : 9.654 86.312 1971 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.89 % Allowed : 21.59 % Favored : 73.52 % 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: -1.12 (0.41), residues: 154 loop : -1.35 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 239 TYR 0.020 0.001 TYR B 132 PHE 0.016 0.002 PHE E 117 TRP 0.006 0.001 TRP C 90 HIS 0.010 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00405 (12965) covalent geometry : angle 0.58885 (17550) hydrogen bonds : bond 0.03087 ( 520) hydrogen bonds : angle 3.57846 ( 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 249 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8658 (tpt90) cc_final: 0.8277 (tpp80) REVERT: C 279 ASP cc_start: 0.8536 (t70) cc_final: 0.8177 (t70) REVERT: B 68 LYS cc_start: 0.8850 (mppt) cc_final: 0.8566 (mptt) REVERT: B 74 MET cc_start: 0.8511 (mtt) cc_final: 0.8101 (mtt) REVERT: B 257 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8418 (mm) REVERT: B 341 GLU cc_start: 0.8544 (tp30) cc_final: 0.8313 (tp30) REVERT: E 74 MET cc_start: 0.8350 (tpp) cc_final: 0.7877 (mpp) REVERT: E 281 HIS cc_start: 0.8527 (p90) cc_final: 0.8174 (p90) REVERT: E 312 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7502 (ttm-80) REVERT: D 118 GLU cc_start: 0.8603 (pp20) cc_final: 0.8181 (pm20) REVERT: D 225 THR cc_start: 0.8818 (t) cc_final: 0.8464 (p) REVERT: D 248 MET cc_start: 0.8637 (mmm) cc_final: 0.8073 (mmm) REVERT: D 290 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8066 (mm-30) REVERT: D 305 ASP cc_start: 0.8551 (t0) cc_final: 0.8028 (t0) REVERT: F 102 ASP cc_start: 0.7870 (m-30) cc_final: 0.7277 (m-30) REVERT: F 207 GLU cc_start: 0.6576 (mm-30) cc_final: 0.6252 (pp20) REVERT: F 275 ASN cc_start: 0.7603 (p0) cc_final: 0.7381 (p0) REVERT: F 345 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8141 (pptt) outliers start: 62 outliers final: 47 residues processed: 236 average time/residue: 0.1100 time to fit residues: 38.1733 Evaluate side-chains 227 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 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 47 GLN Chi-restraints excluded: chain E residue 59 MET 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 245 SER 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 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: 3.9990 chunk 90 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN B 238 ASN E 119 ASN E 337 HIS D 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.118483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.085020 restraints weight = 21669.920| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.32 r_work: 0.3028 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12965 Z= 0.173 Angle : 0.604 9.834 17550 Z= 0.296 Chirality : 0.042 0.166 2045 Planarity : 0.003 0.041 2241 Dihedral : 9.836 86.983 1971 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.73 % Allowed : 22.77 % Favored : 72.50 % 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: -0.03 (0.22), residues: 1648 helix: 1.20 (0.20), residues: 813 sheet: -1.00 (0.41), residues: 154 loop : -1.28 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 239 TYR 0.008 0.001 TYR F 132 PHE 0.012 0.001 PHE B 351 TRP 0.007 0.001 TRP C 90 HIS 0.005 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00413 (12965) covalent geometry : angle 0.60351 (17550) hydrogen bonds : bond 0.03103 ( 520) hydrogen bonds : angle 3.60784 ( 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 247 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: C 59 MET cc_start: 0.8867 (ttm) cc_final: 0.8666 (ttp) REVERT: C 121 ARG cc_start: 0.8666 (tpt90) cc_final: 0.8299 (tpp80) REVERT: C 279 ASP cc_start: 0.8554 (t70) cc_final: 0.8209 (t70) REVERT: B 68 LYS cc_start: 0.8856 (mppt) cc_final: 0.8563 (mptt) REVERT: B 74 MET cc_start: 0.8505 (mtt) cc_final: 0.8086 (mtt) REVERT: B 257 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8420 (mm) REVERT: B 341 GLU cc_start: 0.8549 (tp30) cc_final: 0.8323 (tp30) REVERT: E 45 ARG cc_start: 0.5919 (OUTLIER) cc_final: 0.5135 (ttm-80) REVERT: E 74 MET cc_start: 0.8345 (tpp) cc_final: 0.7875 (mpp) REVERT: E 199 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8302 (ttm-80) REVERT: E 281 HIS cc_start: 0.8514 (p90) cc_final: 0.8131 (p90) REVERT: E 312 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7507 (ttm-80) REVERT: D 118 GLU cc_start: 0.8630 (pp20) cc_final: 0.8237 (pm20) REVERT: D 225 THR cc_start: 0.8829 (t) cc_final: 0.8518 (p) REVERT: D 290 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8118 (mm-30) REVERT: F 102 ASP cc_start: 0.7887 (m-30) cc_final: 0.7678 (m-30) REVERT: F 158 GLN cc_start: 0.6405 (tp40) cc_final: 0.6120 (mm-40) REVERT: F 275 ASN cc_start: 0.7611 (p0) cc_final: 0.7383 (p0) REVERT: F 345 LYS cc_start: 0.8366 (mmtm) cc_final: 0.8103 (pptt) outliers start: 60 outliers final: 47 residues processed: 233 average time/residue: 0.1115 time to fit residues: 37.6372 Evaluate side-chains 229 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN 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 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 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 47 GLN 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 245 SER 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 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: 1.9990 chunk 83 optimal weight: 0.0370 chunk 149 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 0.1980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3718 r_free = 0.3718 target = 0.120624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087231 restraints weight = 21726.263| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.35 r_work: 0.3069 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2960 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= 0.111 Angle : 0.589 10.707 17550 Z= 0.286 Chirality : 0.041 0.162 2045 Planarity : 0.003 0.038 2241 Dihedral : 9.618 86.561 1971 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.94 % Allowed : 23.33 % Favored : 72.73 % 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: 0.13 (0.22), residues: 1648 helix: 1.32 (0.20), residues: 815 sheet: -0.90 (0.41), residues: 154 loop : -1.21 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 239 TYR 0.023 0.001 TYR B 132 PHE 0.011 0.001 PHE D 351 TRP 0.006 0.001 TRP C 90 HIS 0.005 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00257 (12965) covalent geometry : angle 0.58921 (17550) hydrogen bonds : bond 0.02807 ( 520) hydrogen bonds : angle 3.51900 ( 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 245 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8672 (tpt90) cc_final: 0.8298 (tpp80) REVERT: C 279 ASP cc_start: 0.8531 (t70) cc_final: 0.8159 (t70) REVERT: B 68 LYS cc_start: 0.8831 (mppt) cc_final: 0.8533 (mptt) REVERT: B 74 MET cc_start: 0.8466 (mtt) cc_final: 0.8055 (mtt) REVERT: B 257 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8369 (mm) REVERT: B 341 GLU cc_start: 0.8532 (tp30) cc_final: 0.8306 (tp30) REVERT: E 45 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5057 (ttm-80) REVERT: E 74 MET cc_start: 0.8302 (tpp) cc_final: 0.7847 (mpp) REVERT: E 199 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8288 (ttm-80) REVERT: E 286 GLU cc_start: 0.8907 (tp30) cc_final: 0.8498 (tt0) REVERT: E 312 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7499 (ttm-80) REVERT: E 337 HIS cc_start: 0.7440 (m90) cc_final: 0.7171 (m-70) REVERT: D 118 GLU cc_start: 0.8617 (pp20) cc_final: 0.8239 (pm20) REVERT: D 225 THR cc_start: 0.8818 (t) cc_final: 0.8398 (p) REVERT: D 290 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8052 (mm-30) REVERT: F 102 ASP cc_start: 0.7864 (m-30) cc_final: 0.7259 (m-30) REVERT: F 211 MET cc_start: 0.7693 (tmm) cc_final: 0.7434 (tmm) REVERT: F 275 ASN cc_start: 0.7565 (p0) cc_final: 0.7330 (p0) REVERT: F 345 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8093 (pptt) outliers start: 50 outliers final: 42 residues processed: 234 average time/residue: 0.1068 time to fit residues: 36.5904 Evaluate side-chains 226 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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 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 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 47 GLN 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 245 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 238 ASN E 119 ASN D 79 HIS ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS F 124 GLN F 230 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.119241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086062 restraints weight = 21852.845| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.36 r_work: 0.3045 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12965 Z= 0.143 Angle : 0.606 12.012 17550 Z= 0.294 Chirality : 0.042 0.162 2045 Planarity : 0.003 0.039 2241 Dihedral : 9.659 85.971 1971 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.94 % Allowed : 23.80 % Favored : 72.26 % 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: 1.29 (0.20), residues: 820 sheet: -0.76 (0.42), residues: 154 loop : -1.23 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 45 TYR 0.020 0.001 TYR B 132 PHE 0.012 0.001 PHE B 351 TRP 0.007 0.001 TRP E 220 HIS 0.007 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00341 (12965) covalent geometry : angle 0.60558 (17550) hydrogen bonds : bond 0.02916 ( 520) hydrogen bonds : angle 3.52507 ( 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 : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8679 (tpt90) cc_final: 0.8313 (tpp80) REVERT: C 224 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7571 (t0) REVERT: C 279 ASP cc_start: 0.8525 (t70) cc_final: 0.8134 (t70) REVERT: B 68 LYS cc_start: 0.8841 (mppt) cc_final: 0.8529 (mptt) REVERT: B 74 MET cc_start: 0.8469 (mtt) cc_final: 0.8044 (mtt) REVERT: B 257 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 341 GLU cc_start: 0.8544 (tp30) cc_final: 0.8318 (tp30) REVERT: E 45 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5085 (ttm-80) REVERT: E 74 MET cc_start: 0.8299 (tpp) cc_final: 0.7824 (mpp) REVERT: E 199 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8208 (ttm-80) REVERT: E 286 GLU cc_start: 0.8915 (tp30) cc_final: 0.8516 (tt0) REVERT: E 312 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7544 (ttm-80) REVERT: E 337 HIS cc_start: 0.7468 (m90) cc_final: 0.7156 (m-70) REVERT: D 118 GLU cc_start: 0.8630 (pp20) cc_final: 0.8244 (pm20) REVERT: D 121 ARG cc_start: 0.9075 (tpt-90) cc_final: 0.8828 (tpp80) REVERT: D 225 THR cc_start: 0.8811 (t) cc_final: 0.8441 (p) REVERT: D 290 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8058 (mm-30) REVERT: F 102 ASP cc_start: 0.7892 (m-30) cc_final: 0.7679 (m-30) REVERT: F 158 GLN cc_start: 0.6649 (mm-40) cc_final: 0.6420 (mm-40) REVERT: F 275 ASN cc_start: 0.7555 (p0) cc_final: 0.7335 (p0) REVERT: F 345 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8095 (pptt) outliers start: 50 outliers final: 41 residues processed: 227 average time/residue: 0.1116 time to fit residues: 36.6049 Evaluate side-chains 228 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 232 ILE 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 47 GLN 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 245 SER 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 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR 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: 2.9990 chunk 81 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 144 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN D 79 HIS ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.120845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087001 restraints weight = 21560.195| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.38 r_work: 0.3048 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12965 Z= 0.152 Angle : 0.623 12.147 17550 Z= 0.304 Chirality : 0.042 0.191 2045 Planarity : 0.003 0.045 2241 Dihedral : 9.750 86.196 1971 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.10 % Allowed : 23.80 % Favored : 72.10 % 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: 0.15 (0.22), residues: 1648 helix: 1.29 (0.20), residues: 820 sheet: -0.81 (0.41), residues: 159 loop : -1.15 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 280 TYR 0.020 0.001 TYR B 132 PHE 0.011 0.001 PHE E 117 TRP 0.007 0.001 TRP E 220 HIS 0.007 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00365 (12965) covalent geometry : angle 0.62283 (17550) hydrogen bonds : bond 0.02956 ( 520) hydrogen bonds : angle 3.54126 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3083.99 seconds wall clock time: 53 minutes 31.82 seconds (3211.82 seconds total)