Starting phenix.real_space_refine on Thu Jul 31 00:10:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upr_26674/07_2025/7upr_26674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upr_26674/07_2025/7upr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2025/7upr_26674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2025/7upr_26674.map" model { file = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2025/7upr_26674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upr_26674/07_2025/7upr_26674.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 13, 'ARG:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 8, 'GLU:plan': 9, 'HIS:plan': 6} 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: 8.72, per 1000 atoms: 0.68 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: 3.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.26 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: 3.59 Time building geometry restraints manager: 3.79 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 351 or resid 501 throu \ gh 502)) selection = (chain 'D' and (resid 55 through 199 or resid 210 through 351 or resid 501 throu \ gh 502)) selection = (chain 'E' and (resid 55 through 199 or resid 210 through 317 or resid 328 throu \ gh 351 or resid 501 through 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: 1.350 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.960 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.940 ------------------------------------------------------------------------------- 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 : 7.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.000 TRP F 90 HIS 0.003 0.000 HIS B 227 PHE 0.005 0.001 PHE B 216 TYR 0.004 0.000 TYR D 132 ARG 0.001 0.000 ARG C 153 Details of bonding type rmsd hydrogen bonds : bond 0.15788 ( 520) hydrogen bonds : angle 5.01947 ( 1518) covalent geometry : bond 0.00374 (12965) covalent geometry : angle 0.79579 (17550) *********************** 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 : 1.509 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: 0.7053 (mp) REVERT: F 199 ARG cc_start: 0.7762 (ttp-110) cc_final: 0.7559 (ttm110) 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: 0.2584 time to fit residues: 120.4580 Evaluate side-chains 232 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 139 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 119 ASN E 193 GLN E 264 GLN E 332 GLN D 61 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.126762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093657 restraints weight = 21401.709| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.33 r_work: 0.3181 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1468 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= 0.127 Angle : 0.580 10.251 17550 Z= 0.288 Chirality : 0.041 0.149 2045 Planarity : 0.003 0.046 2241 Dihedral : 10.052 81.122 2010 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.65 % Allowed : 19.31 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.20), residues: 1648 helix: 0.06 (0.18), residues: 802 sheet: -2.31 (0.35), residues: 159 loop : -2.07 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 90 HIS 0.006 0.001 HIS B 281 PHE 0.012 0.001 PHE B 351 TYR 0.025 0.001 TYR B 132 ARG 0.004 0.001 ARG D 280 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 520) hydrogen bonds : angle 3.83364 ( 1518) covalent geometry : bond 0.00292 (12965) covalent geometry : angle 0.57973 (17550) *********************** 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: 59 poor density : 213 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7190 (pp) REVERT: C 121 ARG cc_start: 0.8682 (tpt90) cc_final: 0.8298 (tpp80) REVERT: C 279 ASP cc_start: 0.8421 (t70) cc_final: 0.8048 (t70) REVERT: C 280 ARG cc_start: 0.8956 (tmm-80) cc_final: 0.8725 (tmm-80) REVERT: B 68 LYS cc_start: 0.8823 (mppt) cc_final: 0.8621 (mptt) REVERT: B 74 MET cc_start: 0.8381 (mtt) cc_final: 0.8017 (mtt) REVERT: B 79 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7647 (t-90) REVERT: B 184 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7984 (pp) REVERT: B 195 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: B 341 GLU cc_start: 0.8491 (tp30) cc_final: 0.7981 (mm-30) REVERT: E 45 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5117 (ttm-80) REVERT: E 74 MET cc_start: 0.8295 (tpp) cc_final: 0.7752 (mpp) REVERT: E 292 ASP cc_start: 0.8021 (t70) cc_final: 0.7767 (t0) REVERT: D 290 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7987 (mm-30) REVERT: D 305 ASP cc_start: 0.8478 (t0) cc_final: 0.7997 (t0) REVERT: F 98 ASP cc_start: 0.7907 (t0) cc_final: 0.7559 (t0) REVERT: F 102 ASP cc_start: 0.7850 (m-30) cc_final: 0.7414 (m-30) REVERT: F 199 ARG cc_start: 0.7952 (ttp-110) cc_final: 0.7398 (ttm110) REVERT: F 345 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8211 (pptt) outliers start: 59 outliers final: 35 residues processed: 265 average time/residue: 0.2503 time to fit residues: 94.2244 Evaluate side-chains 226 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 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 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 149 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 126 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN ** 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 79 HIS E 119 ASN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.092167 restraints weight = 21798.476| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.37 r_work: 0.3149 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1831 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= 0.122 Angle : 0.550 11.033 17550 Z= 0.272 Chirality : 0.040 0.157 2045 Planarity : 0.003 0.044 2241 Dihedral : 9.639 83.219 1990 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1648 helix: 0.60 (0.19), residues: 805 sheet: -1.96 (0.38), residues: 148 loop : -1.79 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 90 HIS 0.008 0.001 HIS B 281 PHE 0.008 0.001 PHE C 117 TYR 0.019 0.001 TYR B 132 ARG 0.015 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 520) hydrogen bonds : angle 3.67165 ( 1518) covalent geometry : bond 0.00284 (12965) covalent geometry : angle 0.54959 (17550) *********************** 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 251 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7460 (pp) REVERT: C 121 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8280 (tpp80) REVERT: C 279 ASP cc_start: 0.8389 (t70) cc_final: 0.8016 (t70) REVERT: C 280 ARG cc_start: 0.9034 (tmm-80) cc_final: 0.8528 (tmm-80) REVERT: B 68 LYS cc_start: 0.8857 (mppt) cc_final: 0.8560 (mppt) REVERT: B 74 MET cc_start: 0.8411 (mtt) cc_final: 0.8025 (mtt) REVERT: B 79 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7745 (t-90) REVERT: B 195 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: B 341 GLU cc_start: 0.8495 (tp30) cc_final: 0.7986 (mm-30) REVERT: E 45 ARG cc_start: 0.5697 (OUTLIER) cc_final: 0.4947 (ttm-80) REVERT: E 74 MET cc_start: 0.8278 (tpp) cc_final: 0.7766 (mpp) REVERT: E 292 ASP cc_start: 0.8015 (t70) cc_final: 0.7725 (t0) REVERT: D 225 THR cc_start: 0.8667 (t) cc_final: 0.8337 (p) REVERT: D 290 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7936 (mm-30) REVERT: D 305 ASP cc_start: 0.8490 (t0) cc_final: 0.7986 (t0) REVERT: F 98 ASP cc_start: 0.7939 (t0) cc_final: 0.7504 (t0) REVERT: F 102 ASP cc_start: 0.7845 (m-30) cc_final: 0.7342 (m-30) REVERT: F 199 ARG cc_start: 0.7990 (ttp-110) cc_final: 0.7586 (ttm110) REVERT: F 275 ASN cc_start: 0.7792 (p0) cc_final: 0.7568 (p0) REVERT: F 345 LYS cc_start: 0.8394 (mmtm) cc_final: 0.8183 (pptt) outliers start: 55 outliers final: 38 residues processed: 242 average time/residue: 0.2375 time to fit residues: 83.4759 Evaluate side-chains 228 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 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 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 278 VAL 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 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 154 optimal weight: 50.0000 chunk 9 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 47 GLN E 79 HIS E 119 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089690 restraints weight = 21523.125| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.34 r_work: 0.3120 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2082 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 : 0.549 9.947 17550 Z= 0.271 Chirality : 0.041 0.161 2045 Planarity : 0.003 0.044 2241 Dihedral : 9.603 84.219 1983 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.73 % Allowed : 21.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1648 helix: 0.86 (0.20), residues: 807 sheet: -1.43 (0.46), residues: 122 loop : -1.63 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 90 HIS 0.013 0.001 HIS E 281 PHE 0.008 0.001 PHE B 351 TYR 0.024 0.001 TYR B 132 ARG 0.007 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 520) hydrogen bonds : angle 3.58877 ( 1518) covalent geometry : bond 0.00301 (12965) covalent geometry : angle 0.54915 (17550) *********************** 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 258 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8657 (tpt90) cc_final: 0.8285 (tpp80) REVERT: C 279 ASP cc_start: 0.8374 (t70) cc_final: 0.8081 (t70) REVERT: C 280 ARG cc_start: 0.8995 (tmm-80) cc_final: 0.8713 (mmm160) REVERT: B 68 LYS cc_start: 0.8841 (mppt) cc_final: 0.8548 (mppt) REVERT: B 74 MET cc_start: 0.8440 (mtt) cc_final: 0.8051 (mtt) REVERT: B 79 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7764 (t-90) REVERT: B 195 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: B 341 GLU cc_start: 0.8506 (tp30) cc_final: 0.8289 (tp30) REVERT: E 74 MET cc_start: 0.8351 (tpp) cc_final: 0.7867 (mpp) REVERT: E 280 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8090 (tmm160) REVERT: E 292 ASP cc_start: 0.8062 (t70) cc_final: 0.7767 (t0) REVERT: D 225 THR cc_start: 0.8739 (t) cc_final: 0.8426 (p) REVERT: D 290 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7947 (mm-30) REVERT: D 305 ASP cc_start: 0.8505 (t0) cc_final: 0.7998 (t0) REVERT: F 79 HIS cc_start: 0.7954 (m170) cc_final: 0.7739 (m-70) REVERT: F 102 ASP cc_start: 0.7883 (m-30) cc_final: 0.7319 (m-30) REVERT: F 111 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8893 (mp) REVERT: F 199 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7660 (ttm110) REVERT: F 275 ASN cc_start: 0.7743 (p0) cc_final: 0.7488 (p0) REVERT: F 337 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7418 (t-170) REVERT: F 345 LYS cc_start: 0.8394 (mmtm) cc_final: 0.8170 (pptt) outliers start: 60 outliers final: 37 residues processed: 245 average time/residue: 0.2443 time to fit residues: 85.8522 Evaluate side-chains 230 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 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 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 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 111 ILE 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 3 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS E 79 HIS E 119 ASN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.122890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089444 restraints weight = 21609.432| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.36 r_work: 0.3108 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2292 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= 0.119 Angle : 0.549 9.997 17550 Z= 0.270 Chirality : 0.041 0.160 2045 Planarity : 0.003 0.057 2241 Dihedral : 9.439 85.100 1974 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.41 % Allowed : 21.67 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1648 helix: 1.06 (0.20), residues: 813 sheet: -1.45 (0.42), residues: 145 loop : -1.44 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 166 HIS 0.005 0.001 HIS B 281 PHE 0.009 0.001 PHE B 154 TYR 0.007 0.001 TYR B 132 ARG 0.006 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 520) hydrogen bonds : angle 3.54329 ( 1518) covalent geometry : bond 0.00277 (12965) covalent geometry : angle 0.54917 (17550) *********************** 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 260 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8676 (tm-30) REVERT: C 121 ARG cc_start: 0.8639 (tpt90) cc_final: 0.8271 (tpp80) REVERT: C 279 ASP cc_start: 0.8341 (t70) cc_final: 0.8040 (t70) REVERT: C 280 ARG cc_start: 0.9015 (tmm-80) cc_final: 0.8708 (mmm160) REVERT: B 59 MET cc_start: 0.6245 (tpt) cc_final: 0.5952 (tpt) REVERT: B 68 LYS cc_start: 0.8847 (mppt) cc_final: 0.8547 (mppt) REVERT: B 74 MET cc_start: 0.8447 (mtt) cc_final: 0.8039 (mtt) REVERT: B 341 GLU cc_start: 0.8507 (tp30) cc_final: 0.8287 (tp30) REVERT: E 74 MET cc_start: 0.8314 (tpp) cc_final: 0.7836 (mpp) REVERT: E 199 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8499 (ttp80) REVERT: E 292 ASP cc_start: 0.8068 (t70) cc_final: 0.7765 (t0) REVERT: E 312 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7194 (ttm-80) REVERT: D 225 THR cc_start: 0.8763 (t) cc_final: 0.8413 (p) REVERT: D 248 MET cc_start: 0.8586 (mmm) cc_final: 0.7984 (mmm) REVERT: D 290 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7975 (mm-30) REVERT: D 305 ASP cc_start: 0.8482 (t0) cc_final: 0.7973 (t0) REVERT: F 98 ASP cc_start: 0.7928 (t0) cc_final: 0.7446 (t0) REVERT: F 102 ASP cc_start: 0.7871 (m-30) cc_final: 0.7280 (m-30) REVERT: F 199 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7644 (ttm110) REVERT: F 207 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6164 (pp20) REVERT: F 275 ASN cc_start: 0.7712 (p0) cc_final: 0.7503 (p0) REVERT: F 337 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7496 (t-170) REVERT: F 345 LYS cc_start: 0.8395 (mmtm) cc_final: 0.8160 (pptt) outliers start: 56 outliers final: 42 residues processed: 249 average time/residue: 0.2561 time to fit residues: 92.4768 Evaluate side-chains 233 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 C residue 237 THR 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 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 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR 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 150 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS E 119 ASN E 337 HIS D 79 HIS D 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.122324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088520 restraints weight = 21844.100| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.38 r_work: 0.3093 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2483 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= 0.127 Angle : 0.562 11.704 17550 Z= 0.276 Chirality : 0.041 0.160 2045 Planarity : 0.003 0.041 2241 Dihedral : 9.465 85.645 1971 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.28 % Allowed : 21.28 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1648 helix: 1.10 (0.20), residues: 821 sheet: -1.28 (0.43), residues: 145 loop : -1.48 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 90 HIS 0.006 0.001 HIS E 281 PHE 0.010 0.001 PHE B 351 TYR 0.006 0.001 TYR F 132 ARG 0.011 0.000 ARG E 280 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 520) hydrogen bonds : angle 3.52509 ( 1518) covalent geometry : bond 0.00298 (12965) covalent geometry : angle 0.56192 (17550) *********************** 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 258 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: C 121 ARG cc_start: 0.8645 (tpt90) cc_final: 0.8283 (tpp80) REVERT: C 279 ASP cc_start: 0.8496 (t70) cc_final: 0.8165 (t70) REVERT: C 280 ARG cc_start: 0.9008 (tmm-80) cc_final: 0.8725 (mmm160) REVERT: B 68 LYS cc_start: 0.8871 (mppt) cc_final: 0.8567 (mppt) REVERT: B 74 MET cc_start: 0.8465 (mtt) cc_final: 0.8065 (mtt) REVERT: B 257 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8344 (mm) REVERT: B 281 HIS cc_start: 0.8411 (p90) cc_final: 0.8142 (p-80) REVERT: B 341 GLU cc_start: 0.8491 (tp30) cc_final: 0.8268 (tp30) REVERT: E 45 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.5042 (ttm-80) REVERT: E 74 MET cc_start: 0.8321 (tpp) cc_final: 0.7843 (mpp) REVERT: E 121 ARG cc_start: 0.8380 (tpp80) cc_final: 0.8171 (tpp80) REVERT: E 281 HIS cc_start: 0.8516 (p90) cc_final: 0.8282 (p90) REVERT: E 292 ASP cc_start: 0.8051 (t70) cc_final: 0.7765 (t0) REVERT: E 312 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7238 (ttm-80) REVERT: D 225 THR cc_start: 0.8778 (t) cc_final: 0.8463 (p) REVERT: D 290 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7986 (mm-30) REVERT: D 305 ASP cc_start: 0.8487 (t0) cc_final: 0.7969 (t0) REVERT: F 98 ASP cc_start: 0.7922 (t0) cc_final: 0.7403 (t0) REVERT: F 102 ASP cc_start: 0.7884 (m-30) cc_final: 0.7274 (m-30) REVERT: F 111 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8867 (mp) REVERT: F 199 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7691 (ttm110) REVERT: F 207 GLU cc_start: 0.6524 (mm-30) cc_final: 0.6129 (pp20) REVERT: F 275 ASN cc_start: 0.7684 (p0) cc_final: 0.7481 (p0) REVERT: F 345 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8049 (pptt) outliers start: 67 outliers final: 45 residues processed: 243 average time/residue: 0.2644 time to fit residues: 92.4089 Evaluate side-chains 232 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 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 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 111 ILE 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 308 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 125 optimal weight: 5.9990 chunk 154 optimal weight: 40.0000 chunk 92 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.122322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088933 restraints weight = 21477.646| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.35 r_work: 0.3096 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2592 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= 0.114 Angle : 0.555 11.283 17550 Z= 0.272 Chirality : 0.040 0.161 2045 Planarity : 0.003 0.041 2241 Dihedral : 9.399 86.055 1971 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.65 % Allowed : 22.22 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1648 helix: 1.25 (0.20), residues: 814 sheet: -1.06 (0.44), residues: 140 loop : -1.37 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 220 HIS 0.009 0.001 HIS F 79 PHE 0.016 0.001 PHE E 117 TYR 0.006 0.001 TYR F 132 ARG 0.003 0.000 ARG E 280 Details of bonding type rmsd hydrogen bonds : bond 0.02763 ( 520) hydrogen bonds : angle 3.48931 ( 1518) covalent geometry : bond 0.00266 (12965) covalent geometry : angle 0.55497 (17550) *********************** 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 250 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8650 (tpt90) cc_final: 0.8300 (tpp80) REVERT: C 279 ASP cc_start: 0.8509 (t70) cc_final: 0.8156 (t70) REVERT: B 68 LYS cc_start: 0.8879 (mppt) cc_final: 0.8591 (mptt) REVERT: B 74 MET cc_start: 0.8468 (mtt) cc_final: 0.8059 (mtt) REVERT: B 212 MET cc_start: 0.7533 (tmm) cc_final: 0.7265 (tmm) REVERT: B 257 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8314 (mm) REVERT: B 281 HIS cc_start: 0.8413 (p90) cc_final: 0.8142 (p-80) REVERT: B 341 GLU cc_start: 0.8505 (tp30) cc_final: 0.8283 (tp30) REVERT: E 45 ARG cc_start: 0.5833 (OUTLIER) cc_final: 0.5045 (ttm-80) REVERT: E 74 MET cc_start: 0.8287 (tpp) cc_final: 0.7818 (mpp) REVERT: E 121 ARG cc_start: 0.8394 (tpp80) cc_final: 0.8172 (tpp80) REVERT: E 281 HIS cc_start: 0.8513 (p90) cc_final: 0.8168 (p90) REVERT: E 292 ASP cc_start: 0.8041 (t70) cc_final: 0.7757 (t0) REVERT: D 225 THR cc_start: 0.8791 (t) cc_final: 0.8433 (p) REVERT: D 290 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8023 (mm-30) REVERT: D 305 ASP cc_start: 0.8511 (t0) cc_final: 0.7992 (t0) REVERT: F 98 ASP cc_start: 0.7954 (t0) cc_final: 0.7417 (t0) REVERT: F 102 ASP cc_start: 0.7871 (m-30) cc_final: 0.7249 (m-30) REVERT: F 111 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8995 (mp) REVERT: F 199 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7703 (ttm110) REVERT: F 207 GLU cc_start: 0.6422 (mm-30) cc_final: 0.6146 (pp20) REVERT: F 275 ASN cc_start: 0.7669 (p0) cc_final: 0.7456 (p0) REVERT: F 345 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8050 (pptt) outliers start: 59 outliers final: 45 residues processed: 236 average time/residue: 0.2463 time to fit residues: 83.7663 Evaluate side-chains 230 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 201 ARG Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 314 TYR 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 110 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 0.0060 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 79 HIS E 119 ASN E 206 HIS E 337 HIS D 79 HIS F 79 HIS F 230 GLN F 337 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089220 restraints weight = 21588.293| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.36 r_work: 0.3104 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12965 Z= 0.111 Angle : 0.566 10.765 17550 Z= 0.275 Chirality : 0.040 0.159 2045 Planarity : 0.003 0.042 2241 Dihedral : 9.326 85.924 1971 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.33 % Allowed : 23.09 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1648 helix: 1.31 (0.20), residues: 820 sheet: -1.01 (0.42), residues: 154 loop : -1.34 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 90 HIS 0.006 0.001 HIS C 281 PHE 0.020 0.001 PHE C 117 TYR 0.005 0.001 TYR F 132 ARG 0.006 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.02728 ( 520) hydrogen bonds : angle 3.45674 ( 1518) covalent geometry : bond 0.00256 (12965) covalent geometry : angle 0.56647 (17550) *********************** 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 248 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: C 121 ARG cc_start: 0.8661 (tpt90) cc_final: 0.8310 (tpp80) REVERT: C 279 ASP cc_start: 0.8525 (t70) cc_final: 0.8228 (t70) REVERT: B 68 LYS cc_start: 0.8868 (mppt) cc_final: 0.8569 (mppt) REVERT: B 74 MET cc_start: 0.8461 (mtt) cc_final: 0.8062 (mtt) REVERT: B 212 MET cc_start: 0.7515 (tmm) cc_final: 0.7261 (tmm) REVERT: B 257 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8309 (mm) REVERT: B 281 HIS cc_start: 0.8429 (p90) cc_final: 0.8139 (p-80) REVERT: B 341 GLU cc_start: 0.8504 (tp30) cc_final: 0.7997 (mm-30) REVERT: E 74 MET cc_start: 0.8279 (tpp) cc_final: 0.7811 (mpp) REVERT: E 281 HIS cc_start: 0.8540 (p90) cc_final: 0.8224 (p90) REVERT: E 286 GLU cc_start: 0.8902 (tp30) cc_final: 0.8493 (tt0) REVERT: E 292 ASP cc_start: 0.8048 (t70) cc_final: 0.7746 (t0) REVERT: E 312 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7499 (ttm-80) REVERT: E 337 HIS cc_start: 0.7435 (m90) cc_final: 0.7150 (m-70) REVERT: D 225 THR cc_start: 0.8800 (t) cc_final: 0.8479 (p) REVERT: D 290 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8020 (mm-30) REVERT: D 305 ASP cc_start: 0.8511 (t0) cc_final: 0.7997 (t0) REVERT: F 98 ASP cc_start: 0.7959 (t0) cc_final: 0.7421 (t0) REVERT: F 102 ASP cc_start: 0.7902 (m-30) cc_final: 0.7293 (m-30) REVERT: F 111 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8961 (mp) REVERT: F 158 GLN cc_start: 0.6522 (mm-40) cc_final: 0.6234 (mm-40) REVERT: F 199 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7715 (ttm110) REVERT: F 207 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6119 (pp20) REVERT: F 211 MET cc_start: 0.7652 (tmm) cc_final: 0.7402 (tmm) REVERT: F 275 ASN cc_start: 0.7621 (p0) cc_final: 0.7408 (p0) REVERT: F 337 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7561 (t-90) REVERT: F 345 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8136 (pptt) outliers start: 55 outliers final: 44 residues processed: 236 average time/residue: 0.2397 time to fit residues: 82.3004 Evaluate side-chains 234 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 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 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 111 ILE 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 308 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 337 HIS 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 25 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 58 optimal weight: 0.0570 chunk 160 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 overall best weight: 0.5902 ------------------------------------------------------------------------------- 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 79 HIS E 119 ASN D 79 HIS F 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089499 restraints weight = 21505.509| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.34 r_work: 0.3104 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12965 Z= 0.111 Angle : 0.572 10.825 17550 Z= 0.276 Chirality : 0.040 0.159 2045 Planarity : 0.003 0.039 2241 Dihedral : 9.286 85.900 1971 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.18 % Allowed : 23.64 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1648 helix: 1.35 (0.20), residues: 820 sheet: -0.90 (0.42), residues: 154 loop : -1.32 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 90 HIS 0.008 0.001 HIS F 337 PHE 0.010 0.001 PHE D 351 TYR 0.005 0.001 TYR F 132 ARG 0.007 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.02714 ( 520) hydrogen bonds : angle 3.45695 ( 1518) covalent geometry : bond 0.00259 (12965) covalent geometry : angle 0.57194 (17550) *********************** 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 243 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8659 (tpt90) cc_final: 0.8310 (tpp80) REVERT: C 224 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7507 (t0) REVERT: C 279 ASP cc_start: 0.8506 (t70) cc_final: 0.8093 (t70) REVERT: B 68 LYS cc_start: 0.8863 (mppt) cc_final: 0.8559 (mppt) REVERT: B 74 MET cc_start: 0.8462 (mtt) cc_final: 0.8051 (mtt) REVERT: B 212 MET cc_start: 0.7513 (tmm) cc_final: 0.7258 (tmm) REVERT: B 257 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 281 HIS cc_start: 0.8443 (p90) cc_final: 0.8119 (p-80) REVERT: B 341 GLU cc_start: 0.8504 (tp30) cc_final: 0.7997 (mm-30) REVERT: E 45 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5010 (ttm-80) REVERT: E 74 MET cc_start: 0.8276 (tpp) cc_final: 0.7804 (mpp) REVERT: E 199 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8155 (ttm-80) REVERT: E 286 GLU cc_start: 0.8914 (tp30) cc_final: 0.8523 (tt0) REVERT: E 292 ASP cc_start: 0.8050 (t70) cc_final: 0.7732 (t0) REVERT: E 312 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7497 (ttm-80) REVERT: E 337 HIS cc_start: 0.7435 (m90) cc_final: 0.7155 (m-70) REVERT: D 225 THR cc_start: 0.8803 (t) cc_final: 0.8399 (p) REVERT: D 290 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8047 (mm-30) REVERT: D 305 ASP cc_start: 0.8491 (t0) cc_final: 0.7999 (t0) REVERT: F 98 ASP cc_start: 0.7957 (t0) cc_final: 0.7477 (t0) REVERT: F 102 ASP cc_start: 0.7900 (m-30) cc_final: 0.7447 (m-30) REVERT: F 111 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8982 (mp) REVERT: F 158 GLN cc_start: 0.6568 (mm-40) cc_final: 0.6244 (mm-40) REVERT: F 199 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7707 (ttm110) REVERT: F 275 ASN cc_start: 0.7610 (p0) cc_final: 0.7402 (p0) REVERT: F 345 LYS cc_start: 0.8354 (mmtm) cc_final: 0.7995 (pptt) outliers start: 53 outliers final: 42 residues processed: 232 average time/residue: 0.2496 time to fit residues: 82.8421 Evaluate side-chains 231 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 257 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 111 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 148 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 79 HIS E 119 ASN D 79 HIS F 79 HIS F 337 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.123444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.089249 restraints weight = 21522.208| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.43 r_work: 0.3090 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2865 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= 0.125 Angle : 0.580 10.477 17550 Z= 0.282 Chirality : 0.041 0.159 2045 Planarity : 0.003 0.042 2241 Dihedral : 9.337 85.991 1969 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.26 % Allowed : 23.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1648 helix: 1.43 (0.20), residues: 816 sheet: -0.78 (0.42), residues: 154 loop : -1.24 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 90 HIS 0.011 0.001 HIS F 79 PHE 0.011 0.001 PHE B 117 TYR 0.006 0.001 TYR F 132 ARG 0.007 0.000 ARG D 280 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 520) hydrogen bonds : angle 3.45759 ( 1518) covalent geometry : bond 0.00293 (12965) covalent geometry : angle 0.57990 (17550) ********************** 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 245 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8703 (tpt90) cc_final: 0.8347 (tpp80) REVERT: C 224 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7537 (t0) REVERT: C 279 ASP cc_start: 0.8507 (t70) cc_final: 0.8126 (t70) REVERT: B 68 LYS cc_start: 0.8851 (mppt) cc_final: 0.8540 (mppt) REVERT: B 74 MET cc_start: 0.8408 (mtt) cc_final: 0.7996 (mtt) REVERT: B 257 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8184 (mm) REVERT: B 341 GLU cc_start: 0.8484 (tp30) cc_final: 0.8246 (tp30) REVERT: E 45 ARG cc_start: 0.5676 (OUTLIER) cc_final: 0.4889 (ttm-80) REVERT: E 74 MET cc_start: 0.8195 (tpp) cc_final: 0.7725 (mpp) REVERT: E 286 GLU cc_start: 0.8909 (tp30) cc_final: 0.8506 (tt0) REVERT: E 292 ASP cc_start: 0.8043 (t70) cc_final: 0.7711 (t0) REVERT: E 312 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7206 (ttm-80) REVERT: E 337 HIS cc_start: 0.7436 (m90) cc_final: 0.7109 (m-70) REVERT: D 118 GLU cc_start: 0.8614 (pp20) cc_final: 0.8171 (pm20) REVERT: D 225 THR cc_start: 0.8833 (t) cc_final: 0.8425 (p) REVERT: D 290 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8059 (mm-30) REVERT: D 305 ASP cc_start: 0.8445 (t0) cc_final: 0.7952 (t0) REVERT: F 102 ASP cc_start: 0.7842 (m-30) cc_final: 0.7388 (m-30) REVERT: F 158 GLN cc_start: 0.6706 (mm-40) cc_final: 0.6416 (mm-40) REVERT: F 199 ARG cc_start: 0.7977 (ttp-110) cc_final: 0.7615 (ttm110) REVERT: F 337 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7391 (t-90) REVERT: F 345 LYS cc_start: 0.8352 (mmtm) cc_final: 0.7985 (pptt) outliers start: 54 outliers final: 43 residues processed: 234 average time/residue: 0.2560 time to fit residues: 86.1106 Evaluate side-chains 228 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 164 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain 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 308 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 0.2980 chunk 146 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 148 optimal weight: 40.0000 chunk 21 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS E 119 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.123433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.089213 restraints weight = 21490.117| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.43 r_work: 0.3093 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 12965 Z= 0.296 Angle : 0.906 59.197 17550 Z= 0.547 Chirality : 0.068 2.358 2045 Planarity : 0.006 0.226 2241 Dihedral : 9.348 85.992 1969 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.94 % Allowed : 23.40 % Favored : 72.66 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1648 helix: 1.42 (0.20), residues: 816 sheet: -0.78 (0.42), residues: 154 loop : -1.23 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 90 HIS 0.377 0.007 HIS F 337 PHE 0.010 0.001 PHE B 117 TYR 0.005 0.001 TYR C 167 ARG 0.030 0.001 ARG D 280 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 520) hydrogen bonds : angle 3.47242 ( 1518) covalent geometry : bond 0.00520 (12965) covalent geometry : angle 0.90635 (17550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6553.10 seconds wall clock time: 113 minutes 17.85 seconds (6797.85 seconds total)