Starting phenix.real_space_refine on Thu Sep 26 02:43:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/09_2024/7o12_12687.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/09_2024/7o12_12687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/09_2024/7o12_12687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/09_2024/7o12_12687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/09_2024/7o12_12687.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/09_2024/7o12_12687.cif" } resolution = 3.7 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= -0.000 sd= 0.002 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 6 5.49 5 Mg 3 5.21 5 S 36 5.16 5 C 7471 2.51 5 N 2047 2.21 5 O 2128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11691 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3140 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain: "E" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1880 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain breaks: 3 Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 7.45, per 1000 atoms: 0.64 Number of scatterers: 11691 At special positions: 0 Unit cell: (83.106, 168.264, 134.406, 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 36 16.00 P 6 15.00 Mg 3 11.99 O 2128 8.00 N 2047 7.00 C 7471 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: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 48.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.532A pdb=" N MET B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 103 removed outlier: 3.707A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.777A pdb=" N LEU B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 143 removed outlier: 4.001A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.530A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.094A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.784A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.776A pdb=" N GLU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.563A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.671A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.572A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 117 removed outlier: 4.741A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.635A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.775A pdb=" N THR C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.560A pdb=" N MET C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.516A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.503A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.652A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.527A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.817A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.575A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.633A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.593A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.507A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 208 through 213 removed outlier: 3.535A pdb=" N LEU E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 248 through 272 removed outlier: 3.815A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.049A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.524A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.743A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.538A pdb=" N TYR D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.794A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 3.914A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.591A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.560A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.834A pdb=" N MET D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 244 removed outlier: 4.017A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.848A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 26 removed outlier: 5.365A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.282A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 201 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 35 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.787A pdb=" N ILE B 255 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 223 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.787A pdb=" N ILE B 255 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26 removed outlier: 5.978A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 7 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 254 through 258 removed outlier: 3.659A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 37 through 40 removed outlier: 8.000A pdb=" N ARG A 44 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.734A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR A 94 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 199 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.550A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR A 226 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 288 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 252 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE A 290 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASN A 254 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS A 286 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS A 311 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 288 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.541A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 172 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.248A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1476 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: 4.06 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3661 1.33 - 1.45: 2211 1.45 - 1.57: 5972 1.57 - 1.69: 6 1.69 - 1.81: 62 Bond restraints: 11912 Sorted by residual: bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.529 0.171 2.00e-02 2.50e+03 7.30e+01 bond pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 1.700 1.532 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 1.795 1.679 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.680 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" O5' ANP B 402 " pdb=" PA ANP B 402 " ideal model delta sigma weight residual 1.655 1.557 0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 11907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 16012 4.68 - 9.35: 152 9.35 - 14.03: 14 14.03 - 18.70: 5 18.70 - 23.38: 2 Bond angle restraints: 16185 Sorted by residual: angle pdb=" PB ANP C 402 " pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 126.95 103.57 23.38 3.00e+00 1.11e-01 6.07e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 105.67 21.28 3.00e+00 1.11e-01 5.03e+01 angle pdb=" CG1 VAL B 31 " pdb=" CB VAL B 31 " pdb=" CG2 VAL B 31 " ideal model delta sigma weight residual 110.80 99.06 11.74 2.20e+00 2.07e-01 2.85e+01 angle pdb=" PA ANP B 402 " pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 125.41 109.66 15.75 3.00e+00 1.11e-01 2.75e+01 angle pdb=" PA ANP C 402 " pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 125.41 110.62 14.79 3.00e+00 1.11e-01 2.43e+01 ... (remaining 16180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 6547 22.39 - 44.77: 436 44.77 - 67.15: 64 67.15 - 89.54: 19 89.54 - 111.92: 2 Dihedral angle restraints: 7068 sinusoidal: 2809 harmonic: 4259 Sorted by residual: dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU E 73 " pdb=" C LEU E 73 " pdb=" N ALA E 74 " pdb=" CA ALA E 74 " ideal model delta harmonic sigma weight residual 180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA SER D 240 " pdb=" C SER D 240 " pdb=" N LEU D 241 " pdb=" CA LEU D 241 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1620 0.102 - 0.203: 216 0.203 - 0.305: 22 0.305 - 0.407: 6 0.407 - 0.508: 1 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" CB VAL C 187 " pdb=" CA VAL C 187 " pdb=" CG1 VAL C 187 " pdb=" CG2 VAL C 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE B 255 " pdb=" CA ILE B 255 " pdb=" CG1 ILE B 255 " pdb=" CG2 ILE B 255 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1862 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 187 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C VAL B 187 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL B 187 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 188 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO D 67 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 97 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C GLU A 97 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 97 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP A 98 " 0.017 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 31 2.37 - 3.00: 5864 3.00 - 3.63: 18585 3.63 - 4.27: 28575 4.27 - 4.90: 46732 Nonbonded interactions: 99787 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 1.734 2.170 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 1.944 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G ANP B 402 " model vdw 2.095 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2B ANP B 402 " model vdw 2.106 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G ANP C 402 " model vdw 2.107 2.170 ... (remaining 99782 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 132 or resid 136 through \ 228 or resid 245 through 274)) selection = chain 'E' } 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 group one per residue 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: 1.380 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.550 Find NCS groups from input model: 0.490 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.012 0.171 11912 Z= 0.767 Angle : 1.294 23.378 16185 Z= 0.647 Chirality : 0.073 0.508 1865 Planarity : 0.008 0.076 2060 Dihedral : 15.583 111.922 4352 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.82 % Allowed : 9.50 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.32 (0.15), residues: 1493 helix: -4.25 (0.09), residues: 639 sheet: -3.34 (0.30), residues: 194 loop : -2.63 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 45 HIS 0.010 0.002 HIS A 176 PHE 0.022 0.003 PHE A 56 TYR 0.026 0.003 TYR E 93 ARG 0.012 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8580 (tmm) cc_final: 0.8304 (tmm) REVERT: B 61 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8748 (tppt) REVERT: B 200 ILE cc_start: 0.9798 (mt) cc_final: 0.9536 (tt) REVERT: C 46 MET cc_start: 0.9251 (mtm) cc_final: 0.9048 (mtm) REVERT: C 83 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8827 (p) REVERT: C 295 MET cc_start: 0.8078 (mmm) cc_final: 0.7064 (mmm) REVERT: A 62 MET cc_start: 0.8065 (mmp) cc_final: 0.7818 (mmm) REVERT: A 103 THR cc_start: 0.9281 (p) cc_final: 0.9081 (p) REVERT: A 235 LYS cc_start: 0.9338 (mmtt) cc_final: 0.9002 (tppt) REVERT: A 334 LYS cc_start: 0.9540 (tttt) cc_final: 0.8928 (ttmm) REVERT: E 66 MET cc_start: 0.9390 (mmm) cc_final: 0.9083 (mpp) REVERT: E 138 MET cc_start: 0.8877 (tpt) cc_final: 0.8568 (tpp) REVERT: E 171 LYS cc_start: 0.9204 (tttt) cc_final: 0.8974 (tmmt) REVERT: E 213 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9256 (mm) REVERT: E 255 CYS cc_start: 0.9128 (t) cc_final: 0.8716 (t) REVERT: D 82 ASP cc_start: 0.8899 (t70) cc_final: 0.8611 (t0) REVERT: D 83 GLU cc_start: 0.9154 (pt0) cc_final: 0.8734 (pp20) REVERT: D 138 MET cc_start: 0.8849 (tmm) cc_final: 0.8293 (tmm) REVERT: D 171 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8941 (ttmm) REVERT: D 219 ASP cc_start: 0.9182 (m-30) cc_final: 0.8977 (m-30) outliers start: 10 outliers final: 3 residues processed: 104 average time/residue: 0.2750 time to fit residues: 40.4472 Evaluate side-chains 69 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 131 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 0.0040 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS B 115 GLN B 283 HIS C 207 GLN C 263 HIS A 30 GLN A 53 GLN A 77 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS A 179 ASN A 190 ASN A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 417 HIS D 225 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11912 Z= 0.171 Angle : 0.628 9.483 16185 Z= 0.319 Chirality : 0.042 0.179 1865 Planarity : 0.005 0.061 2060 Dihedral : 9.561 135.256 1709 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.13 % Allowed : 13.60 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1493 helix: -1.56 (0.17), residues: 666 sheet: -3.05 (0.31), residues: 199 loop : -1.95 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 253 HIS 0.005 0.001 HIS A 176 PHE 0.010 0.001 PHE E 157 TYR 0.011 0.001 TYR E 221 ARG 0.005 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8657 (tmm) cc_final: 0.8410 (tmm) REVERT: B 61 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8751 (tppt) REVERT: B 200 ILE cc_start: 0.9716 (mt) cc_final: 0.9453 (tt) REVERT: C 16 MET cc_start: 0.8490 (tmm) cc_final: 0.8248 (tmm) REVERT: C 37 HIS cc_start: 0.8420 (m-70) cc_final: 0.7688 (m90) REVERT: C 112 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9378 (mm) REVERT: C 268 LEU cc_start: 0.9592 (mt) cc_final: 0.9368 (mt) REVERT: C 295 MET cc_start: 0.8157 (mmm) cc_final: 0.7551 (mmm) REVERT: A 231 MET cc_start: 0.9083 (mtp) cc_final: 0.8816 (mtp) REVERT: A 235 LYS cc_start: 0.9331 (mmtt) cc_final: 0.8996 (tppt) REVERT: A 334 LYS cc_start: 0.9473 (tttt) cc_final: 0.8971 (ttmm) REVERT: E 143 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8970 (m-10) REVERT: E 212 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8783 (mp) REVERT: E 255 CYS cc_start: 0.8786 (t) cc_final: 0.8345 (t) REVERT: D 82 ASP cc_start: 0.8873 (t70) cc_final: 0.8671 (t0) REVERT: D 83 GLU cc_start: 0.9108 (pt0) cc_final: 0.8647 (pp20) REVERT: D 114 LEU cc_start: 0.8903 (tt) cc_final: 0.8511 (mp) REVERT: D 138 MET cc_start: 0.8965 (tmm) cc_final: 0.8482 (tmm) REVERT: D 170 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: D 255 CYS cc_start: 0.9355 (t) cc_final: 0.8917 (t) outliers start: 26 outliers final: 13 residues processed: 111 average time/residue: 0.2289 time to fit residues: 38.1730 Evaluate side-chains 82 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11912 Z= 0.270 Angle : 0.640 10.677 16185 Z= 0.318 Chirality : 0.042 0.162 1865 Planarity : 0.004 0.037 2060 Dihedral : 7.838 132.920 1708 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.21 % Allowed : 14.99 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.22), residues: 1493 helix: 0.09 (0.20), residues: 663 sheet: -2.80 (0.33), residues: 203 loop : -1.68 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 20 HIS 0.002 0.001 HIS D 108 PHE 0.014 0.001 PHE D 64 TYR 0.007 0.001 TYR E 221 ARG 0.004 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8649 (tmm) cc_final: 0.8372 (tmm) REVERT: B 61 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8740 (tppt) REVERT: C 37 HIS cc_start: 0.8393 (m-70) cc_final: 0.7426 (m90) REVERT: C 112 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9370 (mm) REVERT: C 133 MET cc_start: 0.9327 (mtm) cc_final: 0.9090 (mtm) REVERT: C 268 LEU cc_start: 0.9613 (mt) cc_final: 0.9398 (mt) REVERT: C 295 MET cc_start: 0.8500 (mmm) cc_final: 0.7071 (mmm) REVERT: A 235 LYS cc_start: 0.9338 (mmtt) cc_final: 0.9057 (tppt) REVERT: A 334 LYS cc_start: 0.9505 (tttt) cc_final: 0.9110 (tttp) REVERT: E 212 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8806 (mp) REVERT: E 255 CYS cc_start: 0.8718 (t) cc_final: 0.8341 (t) REVERT: D 82 ASP cc_start: 0.8830 (t70) cc_final: 0.8616 (t0) REVERT: D 83 GLU cc_start: 0.9069 (pt0) cc_final: 0.8631 (pp20) REVERT: D 114 LEU cc_start: 0.8954 (tt) cc_final: 0.8560 (mp) REVERT: D 138 MET cc_start: 0.8985 (tmm) cc_final: 0.8501 (tmm) REVERT: D 170 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: D 201 GLU cc_start: 0.8302 (mp0) cc_final: 0.7938 (mp0) REVERT: D 255 CYS cc_start: 0.9367 (t) cc_final: 0.8957 (t) outliers start: 27 outliers final: 19 residues processed: 96 average time/residue: 0.2106 time to fit residues: 31.5346 Evaluate side-chains 83 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.9990 chunk 101 optimal weight: 0.0370 chunk 69 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11912 Z= 0.155 Angle : 0.567 9.813 16185 Z= 0.280 Chirality : 0.041 0.161 1865 Planarity : 0.003 0.040 2060 Dihedral : 7.387 132.969 1706 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.46 % Allowed : 15.89 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.22), residues: 1493 helix: 0.61 (0.21), residues: 666 sheet: -2.49 (0.32), residues: 218 loop : -1.54 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 236 HIS 0.002 0.000 HIS C 97 PHE 0.010 0.001 PHE E 157 TYR 0.006 0.001 TYR E 221 ARG 0.003 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 73 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8671 (tmm) cc_final: 0.8436 (tmm) REVERT: B 31 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 37 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8067 (m-70) REVERT: B 61 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8766 (tppt) REVERT: C 37 HIS cc_start: 0.8430 (m-70) cc_final: 0.7889 (m-70) REVERT: C 112 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9317 (mm) REVERT: C 261 ASN cc_start: 0.8358 (t0) cc_final: 0.8152 (t0) REVERT: C 268 LEU cc_start: 0.9603 (mt) cc_final: 0.9381 (mt) REVERT: C 295 MET cc_start: 0.8515 (mmm) cc_final: 0.6965 (mmm) REVERT: A 235 LYS cc_start: 0.9344 (mmtt) cc_final: 0.9055 (tppt) REVERT: A 334 LYS cc_start: 0.9457 (tttt) cc_final: 0.9228 (tttp) REVERT: E 212 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8815 (mp) REVERT: E 252 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8951 (tp) REVERT: E 255 CYS cc_start: 0.8738 (t) cc_final: 0.8372 (t) REVERT: D 11 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8118 (mm-30) REVERT: D 83 GLU cc_start: 0.9048 (pt0) cc_final: 0.8649 (pp20) REVERT: D 88 MET cc_start: 0.9246 (ptp) cc_final: 0.8977 (pmm) REVERT: D 114 LEU cc_start: 0.8855 (tt) cc_final: 0.8481 (mp) REVERT: D 138 MET cc_start: 0.9029 (tmm) cc_final: 0.8649 (tmm) REVERT: D 170 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: D 201 GLU cc_start: 0.8277 (mp0) cc_final: 0.8013 (mp0) REVERT: D 255 CYS cc_start: 0.9362 (t) cc_final: 0.8966 (t) outliers start: 30 outliers final: 13 residues processed: 97 average time/residue: 0.1986 time to fit residues: 31.3721 Evaluate side-chains 84 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 170 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11912 Z= 0.242 Angle : 0.592 9.791 16185 Z= 0.293 Chirality : 0.042 0.175 1865 Planarity : 0.003 0.039 2060 Dihedral : 7.216 130.544 1704 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.78 % Allowed : 16.87 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.23), residues: 1493 helix: 1.00 (0.21), residues: 668 sheet: -2.32 (0.33), residues: 218 loop : -1.43 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.013 0.001 HIS A 193 PHE 0.013 0.001 PHE E 157 TYR 0.007 0.001 TYR B 293 ARG 0.002 0.000 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 68 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8674 (tmm) cc_final: 0.8438 (tmm) REVERT: B 61 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8775 (tppt) REVERT: B 295 MET cc_start: 0.8822 (mmm) cc_final: 0.8097 (mtp) REVERT: C 37 HIS cc_start: 0.8498 (m-70) cc_final: 0.7720 (m-70) REVERT: C 46 MET cc_start: 0.9519 (ptp) cc_final: 0.9079 (ptp) REVERT: C 112 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9360 (mm) REVERT: C 133 MET cc_start: 0.9295 (mtm) cc_final: 0.8732 (ptp) REVERT: C 268 LEU cc_start: 0.9597 (mt) cc_final: 0.9379 (mt) REVERT: C 295 MET cc_start: 0.8579 (mmm) cc_final: 0.7300 (mmm) REVERT: A 235 LYS cc_start: 0.9348 (mmtt) cc_final: 0.9073 (tppt) REVERT: A 334 LYS cc_start: 0.9480 (tttt) cc_final: 0.9111 (tttp) REVERT: E 212 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8833 (mp) REVERT: E 252 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8990 (tp) REVERT: E 255 CYS cc_start: 0.8686 (t) cc_final: 0.8349 (t) REVERT: D 11 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 83 GLU cc_start: 0.9002 (pt0) cc_final: 0.8701 (pp20) REVERT: D 114 LEU cc_start: 0.8893 (tt) cc_final: 0.8521 (mp) REVERT: D 138 MET cc_start: 0.9064 (tmm) cc_final: 0.8677 (tmm) REVERT: D 201 GLU cc_start: 0.8440 (mp0) cc_final: 0.8110 (mp0) REVERT: D 255 CYS cc_start: 0.9333 (t) cc_final: 0.8999 (t) outliers start: 34 outliers final: 18 residues processed: 97 average time/residue: 0.2009 time to fit residues: 30.9224 Evaluate side-chains 87 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11912 Z= 0.168 Angle : 0.563 10.394 16185 Z= 0.277 Chirality : 0.041 0.166 1865 Planarity : 0.003 0.038 2060 Dihedral : 7.137 130.321 1704 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.54 % Allowed : 16.95 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.23), residues: 1493 helix: 1.18 (0.21), residues: 671 sheet: -2.16 (0.35), residues: 202 loop : -1.37 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.011 0.001 HIS A 193 PHE 0.010 0.001 PHE E 157 TYR 0.007 0.001 TYR B 291 ARG 0.002 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 67 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8732 (tmm) cc_final: 0.8487 (tmm) REVERT: B 61 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8770 (tppt) REVERT: B 295 MET cc_start: 0.8738 (mmm) cc_final: 0.8059 (mtp) REVERT: C 46 MET cc_start: 0.9466 (ptp) cc_final: 0.8999 (ptp) REVERT: C 112 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9354 (mm) REVERT: C 133 MET cc_start: 0.9268 (mtm) cc_final: 0.8747 (ptp) REVERT: C 268 LEU cc_start: 0.9584 (mt) cc_final: 0.9371 (mt) REVERT: A 235 LYS cc_start: 0.9348 (mmtt) cc_final: 0.9073 (tppt) REVERT: A 334 LYS cc_start: 0.9463 (tttt) cc_final: 0.9241 (tttp) REVERT: E 212 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8808 (mp) REVERT: E 252 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8986 (tp) REVERT: E 255 CYS cc_start: 0.8611 (t) cc_final: 0.8289 (t) REVERT: D 11 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8167 (mm-30) REVERT: D 83 GLU cc_start: 0.8992 (pt0) cc_final: 0.8638 (pp20) REVERT: D 114 LEU cc_start: 0.8854 (tt) cc_final: 0.8473 (mt) REVERT: D 138 MET cc_start: 0.9060 (tmm) cc_final: 0.8674 (tmm) REVERT: D 201 GLU cc_start: 0.8425 (mp0) cc_final: 0.8073 (mp0) REVERT: D 255 CYS cc_start: 0.9321 (t) cc_final: 0.8993 (t) outliers start: 31 outliers final: 22 residues processed: 94 average time/residue: 0.2078 time to fit residues: 31.0780 Evaluate side-chains 90 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 0.0670 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11912 Z= 0.243 Angle : 0.589 9.924 16185 Z= 0.290 Chirality : 0.041 0.157 1865 Planarity : 0.003 0.036 2060 Dihedral : 7.075 129.830 1704 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.95 % Allowed : 17.04 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.23), residues: 1493 helix: 1.37 (0.21), residues: 672 sheet: -2.06 (0.35), residues: 202 loop : -1.34 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 211 HIS 0.004 0.001 HIS A 193 PHE 0.012 0.001 PHE E 157 TYR 0.007 0.001 TYR D 221 ARG 0.002 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 66 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8736 (tmm) cc_final: 0.8473 (tmm) REVERT: B 61 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8771 (tppt) REVERT: C 37 HIS cc_start: 0.8638 (m90) cc_final: 0.7574 (m90) REVERT: C 46 MET cc_start: 0.9456 (ptp) cc_final: 0.8979 (ptp) REVERT: C 112 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9367 (mm) REVERT: C 268 LEU cc_start: 0.9591 (mt) cc_final: 0.9377 (mt) REVERT: A 235 LYS cc_start: 0.9357 (mmtt) cc_final: 0.9074 (tppt) REVERT: A 334 LYS cc_start: 0.9482 (tttt) cc_final: 0.9107 (tttp) REVERT: E 35 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8587 (tt) REVERT: E 213 LEU cc_start: 0.9100 (mt) cc_final: 0.8673 (mt) REVERT: E 252 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8894 (tp) REVERT: E 255 CYS cc_start: 0.8626 (t) cc_final: 0.8309 (t) REVERT: D 11 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8204 (mm-30) REVERT: D 83 GLU cc_start: 0.9015 (pt0) cc_final: 0.8665 (pp20) REVERT: D 114 LEU cc_start: 0.8863 (tt) cc_final: 0.8482 (mt) REVERT: D 138 MET cc_start: 0.9110 (tmm) cc_final: 0.8707 (tmm) REVERT: D 201 GLU cc_start: 0.8486 (mp0) cc_final: 0.8119 (mp0) REVERT: D 255 CYS cc_start: 0.9316 (t) cc_final: 0.9000 (t) outliers start: 36 outliers final: 22 residues processed: 97 average time/residue: 0.2001 time to fit residues: 30.9469 Evaluate side-chains 89 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11912 Z= 0.168 Angle : 0.572 9.874 16185 Z= 0.281 Chirality : 0.041 0.212 1865 Planarity : 0.003 0.039 2060 Dihedral : 7.058 129.748 1704 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.62 % Allowed : 17.61 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.23), residues: 1493 helix: 1.48 (0.21), residues: 670 sheet: -1.83 (0.36), residues: 207 loop : -1.30 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 211 HIS 0.006 0.001 HIS A 193 PHE 0.010 0.001 PHE E 157 TYR 0.009 0.001 TYR C 293 ARG 0.003 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8778 (tmm) cc_final: 0.8519 (tmm) REVERT: B 61 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8771 (tppt) REVERT: B 295 MET cc_start: 0.8512 (mmm) cc_final: 0.8260 (mtp) REVERT: C 46 MET cc_start: 0.9433 (ptp) cc_final: 0.8959 (ptp) REVERT: C 83 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8933 (t) REVERT: C 112 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9339 (mm) REVERT: C 133 MET cc_start: 0.9245 (mtm) cc_final: 0.8751 (ptp) REVERT: C 268 LEU cc_start: 0.9572 (mt) cc_final: 0.9361 (mt) REVERT: A 235 LYS cc_start: 0.9335 (mmtt) cc_final: 0.9074 (tppt) REVERT: A 334 LYS cc_start: 0.9461 (tttt) cc_final: 0.8976 (ttmm) REVERT: E 213 LEU cc_start: 0.9164 (mt) cc_final: 0.8887 (mt) REVERT: E 252 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8922 (tp) REVERT: E 255 CYS cc_start: 0.8628 (t) cc_final: 0.8322 (t) REVERT: D 11 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 83 GLU cc_start: 0.8969 (pt0) cc_final: 0.8638 (pp20) REVERT: D 88 MET cc_start: 0.9305 (ptp) cc_final: 0.8977 (pmm) REVERT: D 114 LEU cc_start: 0.8788 (tt) cc_final: 0.8476 (mt) REVERT: D 138 MET cc_start: 0.9051 (tmm) cc_final: 0.8659 (tmm) REVERT: D 201 GLU cc_start: 0.8450 (mp0) cc_final: 0.8056 (mp0) REVERT: D 255 CYS cc_start: 0.9321 (t) cc_final: 0.9008 (t) outliers start: 32 outliers final: 25 residues processed: 95 average time/residue: 0.1956 time to fit residues: 29.4177 Evaluate side-chains 94 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11912 Z= 0.248 Angle : 0.590 9.613 16185 Z= 0.290 Chirality : 0.042 0.189 1865 Planarity : 0.003 0.038 2060 Dihedral : 7.027 129.423 1704 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.62 % Allowed : 17.53 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.24), residues: 1493 helix: 1.60 (0.21), residues: 670 sheet: -1.85 (0.36), residues: 207 loop : -1.28 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 211 HIS 0.017 0.001 HIS C 37 PHE 0.012 0.001 PHE E 157 TYR 0.008 0.001 TYR D 221 ARG 0.003 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8793 (tmm) cc_final: 0.8534 (tmm) REVERT: B 37 HIS cc_start: 0.8632 (m-70) cc_final: 0.8253 (m-70) REVERT: B 61 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8765 (tppt) REVERT: B 295 MET cc_start: 0.8512 (mmm) cc_final: 0.8085 (mtp) REVERT: C 46 MET cc_start: 0.9427 (ptp) cc_final: 0.8946 (ptp) REVERT: C 83 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.8963 (t) REVERT: C 112 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9352 (mm) REVERT: C 133 MET cc_start: 0.9283 (mtm) cc_final: 0.8732 (ptp) REVERT: C 268 LEU cc_start: 0.9577 (mt) cc_final: 0.9370 (mt) REVERT: A 235 LYS cc_start: 0.9360 (mmtt) cc_final: 0.9106 (tppt) REVERT: A 334 LYS cc_start: 0.9476 (tttt) cc_final: 0.9103 (tttp) REVERT: E 35 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8582 (tt) REVERT: E 213 LEU cc_start: 0.9184 (mt) cc_final: 0.8724 (mt) REVERT: E 219 ASP cc_start: 0.8874 (t0) cc_final: 0.8661 (t0) REVERT: E 252 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8930 (tp) REVERT: E 255 CYS cc_start: 0.8627 (t) cc_final: 0.8323 (t) REVERT: D 11 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8228 (mm-30) REVERT: D 83 GLU cc_start: 0.9037 (pt0) cc_final: 0.8700 (pp20) REVERT: D 88 MET cc_start: 0.9315 (ptp) cc_final: 0.8979 (pmm) REVERT: D 114 LEU cc_start: 0.8772 (tt) cc_final: 0.8485 (mt) REVERT: D 138 MET cc_start: 0.9074 (tmm) cc_final: 0.8667 (tmm) REVERT: D 201 GLU cc_start: 0.8513 (mp0) cc_final: 0.8103 (mp0) REVERT: D 255 CYS cc_start: 0.9320 (t) cc_final: 0.9014 (t) outliers start: 32 outliers final: 26 residues processed: 95 average time/residue: 0.1951 time to fit residues: 29.3090 Evaluate side-chains 95 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11912 Z= 0.203 Angle : 0.581 9.634 16185 Z= 0.285 Chirality : 0.042 0.179 1865 Planarity : 0.003 0.039 2060 Dihedral : 7.022 129.295 1704 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.46 % Allowed : 17.85 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.24), residues: 1493 helix: 1.65 (0.21), residues: 670 sheet: -1.86 (0.36), residues: 207 loop : -1.27 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 240 HIS 0.008 0.001 HIS C 37 PHE 0.011 0.001 PHE E 157 TYR 0.008 0.001 TYR C 291 ARG 0.004 0.000 ARG B 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8798 (tmm) cc_final: 0.8529 (tmm) REVERT: B 37 HIS cc_start: 0.8605 (m-70) cc_final: 0.8310 (m-70) REVERT: B 61 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8767 (tppt) REVERT: B 83 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8526 (t) REVERT: B 295 MET cc_start: 0.8542 (mmm) cc_final: 0.8094 (mtp) REVERT: C 46 MET cc_start: 0.9423 (ptp) cc_final: 0.8943 (ptp) REVERT: C 83 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.8969 (t) REVERT: C 112 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9354 (mm) REVERT: C 133 MET cc_start: 0.9279 (mtm) cc_final: 0.8729 (ptp) REVERT: C 268 LEU cc_start: 0.9573 (mt) cc_final: 0.9365 (mt) REVERT: A 235 LYS cc_start: 0.9360 (mmtt) cc_final: 0.9103 (tppt) REVERT: A 334 LYS cc_start: 0.9464 (tttt) cc_final: 0.9237 (tttp) REVERT: E 35 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8588 (tt) REVERT: E 213 LEU cc_start: 0.9235 (mt) cc_final: 0.8789 (mt) REVERT: E 219 ASP cc_start: 0.8871 (t0) cc_final: 0.8666 (t0) REVERT: E 252 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8930 (tp) REVERT: E 255 CYS cc_start: 0.8624 (t) cc_final: 0.8324 (t) REVERT: D 11 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8235 (mm-30) REVERT: D 83 GLU cc_start: 0.9000 (pt0) cc_final: 0.8663 (pp20) REVERT: D 88 MET cc_start: 0.9306 (ptp) cc_final: 0.8989 (pmm) REVERT: D 114 LEU cc_start: 0.8700 (tt) cc_final: 0.8442 (mp) REVERT: D 138 MET cc_start: 0.9068 (tmm) cc_final: 0.8668 (tmm) REVERT: D 201 GLU cc_start: 0.8503 (mp0) cc_final: 0.8083 (mp0) REVERT: D 255 CYS cc_start: 0.9319 (t) cc_final: 0.9015 (t) outliers start: 30 outliers final: 25 residues processed: 92 average time/residue: 0.1998 time to fit residues: 29.2123 Evaluate side-chains 95 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 177 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.045297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.034977 restraints weight = 75279.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.036158 restraints weight = 39508.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036909 restraints weight = 26134.283| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11912 Z= 0.200 Angle : 0.574 9.606 16185 Z= 0.282 Chirality : 0.042 0.166 1865 Planarity : 0.003 0.039 2060 Dihedral : 7.010 129.209 1704 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.54 % Allowed : 18.02 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.23), residues: 1493 helix: 1.59 (0.21), residues: 684 sheet: -1.86 (0.36), residues: 207 loop : -1.40 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 240 HIS 0.010 0.001 HIS C 37 PHE 0.011 0.001 PHE E 157 TYR 0.011 0.001 TYR C 291 ARG 0.002 0.000 ARG B 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.65 seconds wall clock time: 40 minutes 1.66 seconds (2401.66 seconds total)