Starting phenix.real_space_refine on Sun Aug 24 16:43:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiu_60605/08_2025/9iiu_60605_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiu_60605/08_2025/9iiu_60605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iiu_60605/08_2025/9iiu_60605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiu_60605/08_2025/9iiu_60605.map" model { file = "/net/cci-nas-00/data/ceres_data/9iiu_60605/08_2025/9iiu_60605_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiu_60605/08_2025/9iiu_60605_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.045 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 6 5.49 5 Mg 35 5.21 5 S 71 5.16 5 C 14781 2.51 5 N 3093 2.21 5 O 3464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21452 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2355 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 13, 'TRANS': 287} Chain breaks: 1 Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3755 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain: "C" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3431 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 24, 'TRANS': 413} Chain breaks: 1 Chain: "D" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2671 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1806 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 4, 'ASP:plan': 5, 'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 5, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "H" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 532 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain breaks: 1 Chain: "I" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "J" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 232 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "L" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 290 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "M" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 210 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "T" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 198 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "V" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 224 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "X" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 214 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "Z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "A" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 419 Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1, 'LHG': 1, 'LMG': 1, 'PHO': 1, 'SQD': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1274 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 1, 'LMG': 2} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1166 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 2, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 551 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 3, 'LMG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.32, per 1000 atoms: 0.20 Number of scatterers: 21452 At special positions: 0 Unit cell: (132, 106, 144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 71 16.00 P 6 15.00 Mg 35 11.99 O 3464 8.00 N 3093 7.00 C 14781 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=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 863.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 9 sheets defined 67.9% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 30 through 54 removed outlier: 4.013A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.897A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 4.115A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 267 through 295 Proline residue: A 279 - end of helix removed outlier: 3.626A pdb=" N PHE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 333 Processing helix chain 'B' and resid 7 through 13 Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.818A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 219 removed outlier: 3.889A pdb=" N ILE B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 233 through 259 removed outlier: 4.008A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.653A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 322 Proline residue: B 319 - end of helix removed outlier: 3.934A pdb=" N GLY B 322 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 6.102A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.540A pdb=" N GLY C 73 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.715A pdb=" N HIS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.540A pdb=" N GLU C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 119 Processing helix chain 'C' and resid 141 through 169 Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.818A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.509A pdb=" N CYS C 213 " --> pdb=" O GLY C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 241 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.648A pdb=" N LEU C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 347 removed outlier: 3.786A pdb=" N ARG C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 54 removed outlier: 3.929A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 108 through 136 removed outlier: 3.916A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.056A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.727A pdb=" N PHE D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 188 Processing helix chain 'D' and resid 194 through 221 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 3.826A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 removed outlier: 4.574A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'E' and resid 9 through 16 Processing helix chain 'E' and resid 16 through 25 removed outlier: 4.054A pdb=" N TRP E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 71 through 80 removed outlier: 3.856A pdb=" N GLN E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 41 Proline residue: F 28 - end of helix removed outlier: 3.811A pdb=" N PHE F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 142 Processing helix chain 'G' and resid 166 through 178 removed outlier: 4.040A pdb=" N GLN G 171 " --> pdb=" O ALA G 167 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY G 178 " --> pdb=" O LYS G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'G' and resid 218 through 232 removed outlier: 3.629A pdb=" N MET G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 263 removed outlier: 4.030A pdb=" N LYS G 250 " --> pdb=" O THR G 246 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 279 Processing helix chain 'G' and resid 283 through 289 Processing helix chain 'G' and resid 290 through 292 No H-bonds generated for 'chain 'G' and resid 290 through 292' Processing helix chain 'G' and resid 293 through 299 removed outlier: 4.025A pdb=" N ASN G 299 " --> pdb=" O LYS G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 310 removed outlier: 4.203A pdb=" N GLN G 303 " --> pdb=" O ASN G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 323 Processing helix chain 'H' and resid 24 through 31 Processing helix chain 'H' and resid 32 through 35 Processing helix chain 'H' and resid 46 through 69 Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'I' and resid 2 through 26 Processing helix chain 'J' and resid 11 through 36 Processing helix chain 'K' and resid 12 through 17 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 18 through 25 removed outlier: 3.678A pdb=" N VAL K 22 " --> pdb=" O PHE K 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 44 Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.504A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 29 Proline residue: M 18 - end of helix Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'V' and resid 3 through 29 removed outlier: 4.069A pdb=" N GLY V 19 " --> pdb=" O VAL V 15 " (cutoff:3.500A) Proline residue: V 20 - end of helix Processing helix chain 'X' and resid 66 through 95 removed outlier: 3.936A pdb=" N LYS X 95 " --> pdb=" O THR X 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 29 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 36 through 61 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 340 removed outlier: 3.877A pdb=" N ILE B 336 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.555A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 409 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA8, first strand: chain 'D' and resid 77 through 78 removed outlier: 3.525A pdb=" N PHE D 173 " --> pdb=" O VAL D 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 73 through 75 removed outlier: 4.105A pdb=" N TYR G 147 " --> pdb=" O SER G 119 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU G 117 " --> pdb=" O LYS G 149 " (cutoff:3.500A) 1117 hydrogen bonds defined for protein. 3183 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: 2.63 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 8542 1.39 - 1.57: 13459 1.57 - 1.75: 15 1.75 - 1.92: 121 1.92 - 2.10: 144 Bond restraints: 22281 Sorted by residual: bond pdb=" C6 SQD A 407 " pdb=" S SQD A 407 " ideal model delta sigma weight residual 1.840 1.662 0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C7 LHG D 410 " pdb=" O7 LHG D 410 " ideal model delta sigma weight residual 1.329 1.457 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C7 LHG D 408 " pdb=" O7 LHG D 408 " ideal model delta sigma weight residual 1.329 1.457 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C1B DGD C 517 " pdb=" O2G DGD C 517 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C7 LHG B 521 " pdb=" O7 LHG B 521 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.03e+01 ... (remaining 22276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 30119 3.66 - 7.31: 454 7.31 - 10.97: 62 10.97 - 14.63: 42 14.63 - 18.28: 28 Bond angle restraints: 30705 Sorted by residual: angle pdb=" N PRO G 78 " pdb=" CA PRO G 78 " pdb=" CB PRO G 78 " ideal model delta sigma weight residual 103.36 110.28 -6.92 8.80e-01 1.29e+00 6.18e+01 angle pdb=" N PRO G 80 " pdb=" CA PRO G 80 " pdb=" CB PRO G 80 " ideal model delta sigma weight residual 103.25 110.92 -7.67 1.05e+00 9.07e-01 5.34e+01 angle pdb=" N PRO G 100 " pdb=" CA PRO G 100 " pdb=" CB PRO G 100 " ideal model delta sigma weight residual 103.20 109.97 -6.77 9.50e-01 1.11e+00 5.08e+01 angle pdb=" N PRO G 111 " pdb=" CA PRO G 111 " pdb=" CB PRO G 111 " ideal model delta sigma weight residual 103.25 110.52 -7.27 1.05e+00 9.07e-01 4.80e+01 angle pdb=" NB CLA B 511 " pdb="MG CLA B 511 " pdb=" ND CLA B 511 " ideal model delta sigma weight residual 176.90 158.62 18.28 3.00e+00 1.11e-01 3.71e+01 ... (remaining 30700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 11558 34.07 - 68.15: 446 68.15 - 102.22: 39 102.22 - 136.29: 15 136.29 - 170.37: 1 Dihedral angle restraints: 12059 sinusoidal: 5560 harmonic: 6499 Sorted by residual: dihedral pdb=" C3A DGD C 517 " pdb=" C1A DGD C 517 " pdb=" C2A DGD C 517 " pdb=" O1A DGD C 517 " ideal model delta sinusoidal sigma weight residual 335.78 165.41 170.37 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C4D PHO D 402 " pdb=" CBD PHO D 402 " pdb=" CHA PHO D 402 " pdb=" CGD PHO D 402 " ideal model delta sinusoidal sigma weight residual 243.52 111.54 131.98 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C3D PHO D 402 " pdb=" CAD PHO D 402 " pdb=" CBD PHO D 402 " pdb=" CGD PHO D 402 " ideal model delta sinusoidal sigma weight residual 240.94 109.52 131.42 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 12056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2427 0.048 - 0.097: 459 0.097 - 0.145: 105 0.145 - 0.194: 11 0.194 - 0.242: 7 Chirality restraints: 3009 Sorted by residual: chirality pdb=" CA PRO G 100 " pdb=" N PRO G 100 " pdb=" C PRO G 100 " pdb=" CB PRO G 100 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C1E DGD C 517 " pdb=" C2E DGD C 517 " pdb=" O5D DGD C 517 " pdb=" O6E DGD C 517 " both_signs ideal model delta sigma weight residual False -2.19 -2.41 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C2 LHG D 411 " pdb=" C1 LHG D 411 " pdb=" C3 LHG D 411 " pdb=" O2 LHG D 411 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 3006 not shown) Planarity restraints: 3815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 402 " -0.122 2.00e-02 2.50e+03 1.24e-01 1.24e+03 pdb=" ND PHO D 402 " -0.340 2.00e-02 2.50e+03 pdb=" C1A PHO D 402 " -0.009 2.00e-02 2.50e+03 pdb=" C1B PHO D 402 " -0.045 2.00e-02 2.50e+03 pdb=" C1C PHO D 402 " -0.037 2.00e-02 2.50e+03 pdb=" C1D PHO D 402 " -0.063 2.00e-02 2.50e+03 pdb=" C2A PHO D 402 " -0.313 2.00e-02 2.50e+03 pdb=" C2B PHO D 402 " 0.015 2.00e-02 2.50e+03 pdb=" C2C PHO D 402 " -0.013 2.00e-02 2.50e+03 pdb=" C2D PHO D 402 " 0.011 2.00e-02 2.50e+03 pdb=" C3A PHO D 402 " 0.140 2.00e-02 2.50e+03 pdb=" C3B PHO D 402 " -0.009 2.00e-02 2.50e+03 pdb=" C3C PHO D 402 " 0.046 2.00e-02 2.50e+03 pdb=" C3D PHO D 402 " -0.016 2.00e-02 2.50e+03 pdb=" C4A PHO D 402 " 0.118 2.00e-02 2.50e+03 pdb=" C4B PHO D 402 " -0.092 2.00e-02 2.50e+03 pdb=" C4C PHO D 402 " 0.050 2.00e-02 2.50e+03 pdb=" C4D PHO D 402 " -0.115 2.00e-02 2.50e+03 pdb=" CAB PHO D 402 " 0.052 2.00e-02 2.50e+03 pdb=" CAC PHO D 402 " 0.101 2.00e-02 2.50e+03 pdb=" CAD PHO D 402 " 0.015 2.00e-02 2.50e+03 pdb=" CBD PHO D 402 " 0.263 2.00e-02 2.50e+03 pdb=" CHA PHO D 402 " 0.045 2.00e-02 2.50e+03 pdb=" CHB PHO D 402 " -0.020 2.00e-02 2.50e+03 pdb=" CHC PHO D 402 " -0.099 2.00e-02 2.50e+03 pdb=" CHD PHO D 402 " 0.113 2.00e-02 2.50e+03 pdb=" CMB PHO D 402 " 0.119 2.00e-02 2.50e+03 pdb=" CMC PHO D 402 " -0.020 2.00e-02 2.50e+03 pdb=" CMD PHO D 402 " 0.109 2.00e-02 2.50e+03 pdb=" NA PHO D 402 " 0.229 2.00e-02 2.50e+03 pdb=" NC PHO D 402 " 0.007 2.00e-02 2.50e+03 pdb=" OBD PHO D 402 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " -0.095 2.00e-02 2.50e+03 1.09e-01 9.52e+02 pdb=" ND PHO A 404 " -0.073 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " 0.001 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " -0.035 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " -0.025 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " -0.007 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " 0.062 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " 0.113 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " -0.058 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " 0.030 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " -0.306 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " 0.133 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " -0.045 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " 0.057 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " -0.184 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " -0.006 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " 0.002 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " 0.013 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " 0.243 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " -0.064 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " 0.089 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " 0.141 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " 0.051 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " -0.123 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " -0.035 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " 0.033 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " 0.200 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " -0.105 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " 0.049 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " -0.149 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " 0.014 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CLA B 511 " -0.077 2.00e-02 2.50e+03 1.49e-01 2.78e+02 pdb=" ND CLA B 511 " -0.074 2.00e-02 2.50e+03 pdb=" NA CLA B 511 " -0.075 2.00e-02 2.50e+03 pdb=" NC CLA B 511 " -0.072 2.00e-02 2.50e+03 pdb="MG CLA B 511 " 0.298 2.00e-02 2.50e+03 ... (remaining 3812 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 205 2.59 - 3.17: 17915 3.17 - 3.74: 35747 3.74 - 4.32: 51125 4.32 - 4.90: 85728 Nonbonded interactions: 190720 Sorted by model distance: nonbonded pdb=" OG1 THR A 286 " pdb=" O1D CLA A 402 " model vdw 2.010 3.040 nonbonded pdb=" NH1 ARG B 272 " pdb=" OD2 ASP B 276 " model vdw 2.097 3.120 nonbonded pdb=" O VAL K 43 " pdb=" OG SER K 44 " model vdw 2.106 3.040 nonbonded pdb=" O ARG B 7 " pdb=" OG1 THR B 10 " model vdw 2.111 3.040 nonbonded pdb=" OE2 GLU L 12 " pdb=" O2 LHG L 101 " model vdw 2.122 3.040 ... (remaining 190715 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 16.950 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.008 0.178 22309 Z= 0.457 Angle : 1.187 18.283 30705 Z= 0.446 Chirality : 0.042 0.242 3009 Planarity : 0.013 0.149 3815 Dihedral : 17.695 170.367 7911 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.92 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.18), residues: 2259 helix: 1.88 (0.14), residues: 1364 sheet: -0.56 (1.01), residues: 35 loop : -0.26 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 352 TYR 0.010 0.001 TYR C 262 PHE 0.020 0.001 PHE B 246 TRP 0.012 0.001 TRP A 131 HIS 0.005 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00687 (22281) covalent geometry : angle 1.18674 (30705) hydrogen bonds : bond 0.11706 ( 1117) hydrogen bonds : angle 5.75157 ( 3183) Misc. bond : bond 0.09051 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: B 14 ASN cc_start: 0.8120 (m-40) cc_final: 0.7894 (m110) REVERT: B 222 SER cc_start: 0.8453 (p) cc_final: 0.8159 (m) REVERT: C 290 TYR cc_start: 0.8837 (m-80) cc_final: 0.8416 (m-80) REVERT: D 16 ASP cc_start: 0.8487 (m-30) cc_final: 0.8233 (m-30) REVERT: F 42 ILE cc_start: 0.8993 (tt) cc_final: 0.8773 (tt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.4797 time to fit residues: 137.8401 Evaluate side-chains 205 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS B 318 ASN G 195 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101107 restraints weight = 28394.409| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.93 r_work: 0.3189 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.321 22309 Z= 0.139 Angle : 0.583 9.232 30705 Z= 0.272 Chirality : 0.043 0.280 3009 Planarity : 0.005 0.065 3815 Dihedral : 16.377 174.341 4165 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.34 % Rotamer: Outliers : 1.11 % Allowed : 7.86 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.18), residues: 2259 helix: 1.80 (0.14), residues: 1393 sheet: -0.88 (0.89), residues: 39 loop : -0.11 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 272 TYR 0.014 0.001 TYR G 249 PHE 0.029 0.001 PHE B 246 TRP 0.018 0.001 TRP F 19 HIS 0.012 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00302 (22281) covalent geometry : angle 0.58283 (30705) hydrogen bonds : bond 0.04197 ( 1117) hydrogen bonds : angle 4.85985 ( 3183) Misc. bond : bond 0.07024 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8739 (mt-10) REVERT: C 290 TYR cc_start: 0.8800 (m-80) cc_final: 0.8435 (m-80) REVERT: C 444 GLU cc_start: 0.7255 (pm20) cc_final: 0.6926 (pm20) REVERT: D 16 ASP cc_start: 0.8514 (m-30) cc_final: 0.7986 (m-30) REVERT: D 224 GLU cc_start: 0.8176 (tt0) cc_final: 0.7828 (mt-10) REVERT: E 71 ASN cc_start: 0.8180 (t0) cc_final: 0.7815 (t0) REVERT: E 74 GLU cc_start: 0.7773 (pt0) cc_final: 0.7510 (mm-30) REVERT: F 42 ILE cc_start: 0.8869 (tt) cc_final: 0.8652 (tt) REVERT: G 135 ILE cc_start: 0.8613 (tt) cc_final: 0.8403 (pp) REVERT: G 286 GLN cc_start: 0.7893 (tt0) cc_final: 0.7610 (tt0) REVERT: K 15 TYR cc_start: 0.8693 (m-80) cc_final: 0.8477 (m-80) REVERT: T 23 PHE cc_start: 0.5885 (m-80) cc_final: 0.5674 (m-80) outliers start: 20 outliers final: 9 residues processed: 246 average time/residue: 0.4545 time to fit residues: 130.8725 Evaluate side-chains 223 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 213 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain Z residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 148 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 167 optimal weight: 0.0670 chunk 142 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS C 310 GLN D 186 GLN G 171 GLN G 195 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098211 restraints weight = 28740.047| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.91 r_work: 0.3151 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.274 22309 Z= 0.167 Angle : 0.568 9.126 30705 Z= 0.268 Chirality : 0.043 0.345 3009 Planarity : 0.005 0.064 3815 Dihedral : 16.030 170.599 4165 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.61 % Favored : 97.21 % Rotamer: Outliers : 1.90 % Allowed : 11.04 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.18), residues: 2259 helix: 1.67 (0.14), residues: 1392 sheet: -0.76 (0.93), residues: 35 loop : -0.16 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 352 TYR 0.026 0.001 TYR G 137 PHE 0.027 0.001 PHE G 302 TRP 0.023 0.001 TRP F 19 HIS 0.014 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00384 (22281) covalent geometry : angle 0.56836 (30705) hydrogen bonds : bond 0.04034 ( 1117) hydrogen bonds : angle 4.72931 ( 3183) Misc. bond : bond 0.06138 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8765 (mt-10) REVERT: B 350 GLU cc_start: 0.8064 (mp0) cc_final: 0.7676 (mt-10) REVERT: C 310 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: C 444 GLU cc_start: 0.7190 (pm20) cc_final: 0.6827 (pm20) REVERT: D 16 ASP cc_start: 0.8570 (m-30) cc_final: 0.8074 (m-30) REVERT: D 20 ASP cc_start: 0.8624 (m-30) cc_final: 0.8316 (m-30) REVERT: E 71 ASN cc_start: 0.8137 (t0) cc_final: 0.7920 (t0) REVERT: F 42 ILE cc_start: 0.8865 (tt) cc_final: 0.8636 (tt) REVERT: G 137 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7767 (t80) REVERT: G 206 MET cc_start: 0.8144 (mtm) cc_final: 0.7242 (ttp) REVERT: G 225 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7225 (mm-30) REVERT: G 277 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8017 (mtt) REVERT: G 284 TYR cc_start: 0.8169 (m-10) cc_final: 0.7951 (m-10) REVERT: G 286 GLN cc_start: 0.7915 (tt0) cc_final: 0.7675 (tt0) REVERT: T 23 PHE cc_start: 0.6014 (m-80) cc_final: 0.5814 (m-80) REVERT: Z 44 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5684 (mm) outliers start: 34 outliers final: 15 residues processed: 237 average time/residue: 0.4372 time to fit residues: 121.5216 Evaluate side-chains 224 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN G 195 GLN G 303 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097479 restraints weight = 28510.058| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.90 r_work: 0.3148 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 22309 Z= 0.165 Angle : 0.561 9.144 30705 Z= 0.264 Chirality : 0.042 0.306 3009 Planarity : 0.005 0.062 3815 Dihedral : 15.936 169.240 4165 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.74 % Favored : 97.08 % Rotamer: Outliers : 2.34 % Allowed : 12.54 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2259 helix: 1.64 (0.14), residues: 1392 sheet: -0.86 (0.92), residues: 35 loop : -0.22 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 311 TYR 0.019 0.001 TYR G 137 PHE 0.026 0.001 PHE G 302 TRP 0.024 0.001 TRP F 19 HIS 0.007 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00378 (22281) covalent geometry : angle 0.56052 (30705) hydrogen bonds : bond 0.03925 ( 1117) hydrogen bonds : angle 4.69440 ( 3183) Misc. bond : bond 0.05599 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: B 352 ARG cc_start: 0.8426 (mpp80) cc_final: 0.8120 (ptt180) REVERT: C 290 TYR cc_start: 0.8742 (m-80) cc_final: 0.8437 (m-80) REVERT: C 371 ASP cc_start: 0.7658 (t0) cc_final: 0.7356 (t0) REVERT: C 444 GLU cc_start: 0.7270 (pm20) cc_final: 0.6858 (pm20) REVERT: D 16 ASP cc_start: 0.8635 (m-30) cc_final: 0.8104 (m-30) REVERT: D 20 ASP cc_start: 0.8719 (m-30) cc_final: 0.8433 (m-30) REVERT: E 54 GLU cc_start: 0.8810 (pt0) cc_final: 0.8497 (pm20) REVERT: E 74 GLU cc_start: 0.7688 (pt0) cc_final: 0.7440 (mm-30) REVERT: F 42 ILE cc_start: 0.8897 (tt) cc_final: 0.8673 (tt) REVERT: G 206 MET cc_start: 0.8405 (mtm) cc_final: 0.7448 (ttp) REVERT: G 211 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7825 (pp) REVERT: G 225 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7050 (mm-30) REVERT: G 254 TYR cc_start: 0.8242 (t80) cc_final: 0.7814 (t80) REVERT: G 277 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7923 (mtt) REVERT: G 284 TYR cc_start: 0.8181 (m-10) cc_final: 0.7974 (m-10) REVERT: G 286 GLN cc_start: 0.7924 (tt0) cc_final: 0.7280 (tp40) REVERT: T 23 PHE cc_start: 0.6086 (m-80) cc_final: 0.5825 (m-80) REVERT: Z 44 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5663 (mm) outliers start: 42 outliers final: 19 residues processed: 231 average time/residue: 0.4628 time to fit residues: 125.8246 Evaluate side-chains 223 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 44 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 140 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 168 optimal weight: 50.0000 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 0.0010 chunk 203 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 169 optimal weight: 50.0000 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 310 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN G 195 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098677 restraints weight = 28346.671| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.90 r_work: 0.3152 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 22309 Z= 0.146 Angle : 0.544 9.644 30705 Z= 0.257 Chirality : 0.041 0.314 3009 Planarity : 0.005 0.069 3815 Dihedral : 15.698 168.396 4165 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.83 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 13.32 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.18), residues: 2259 helix: 1.65 (0.14), residues: 1395 sheet: -0.82 (0.92), residues: 35 loop : -0.21 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 257 TYR 0.016 0.001 TYR C 262 PHE 0.023 0.001 PHE G 302 TRP 0.026 0.001 TRP F 19 HIS 0.006 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00331 (22281) covalent geometry : angle 0.54437 (30705) hydrogen bonds : bond 0.03850 ( 1117) hydrogen bonds : angle 4.62018 ( 3183) Misc. bond : bond 0.05001 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8728 (mt-10) REVERT: A 260 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.6278 (m-10) REVERT: B 352 ARG cc_start: 0.8425 (mpp80) cc_final: 0.8062 (mpp80) REVERT: C 290 TYR cc_start: 0.8744 (m-80) cc_final: 0.8435 (m-80) REVERT: C 310 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: C 371 ASP cc_start: 0.7684 (t0) cc_final: 0.7169 (t0) REVERT: C 373 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6603 (mm-40) REVERT: C 444 GLU cc_start: 0.7241 (pm20) cc_final: 0.6816 (pm20) REVERT: D 16 ASP cc_start: 0.8658 (m-30) cc_final: 0.8064 (m-30) REVERT: D 20 ASP cc_start: 0.8728 (m-30) cc_final: 0.8392 (m-30) REVERT: D 142 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8297 (t0) REVERT: D 224 GLU cc_start: 0.8154 (tt0) cc_final: 0.7832 (mt-10) REVERT: E 71 ASN cc_start: 0.8185 (t0) cc_final: 0.7962 (t0) REVERT: F 42 ILE cc_start: 0.8891 (tt) cc_final: 0.8675 (tt) REVERT: G 206 MET cc_start: 0.8200 (mtm) cc_final: 0.7231 (ttp) REVERT: G 211 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7790 (pp) REVERT: G 225 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7057 (mm-30) REVERT: G 263 LEU cc_start: 0.8620 (tp) cc_final: 0.7994 (tt) REVERT: G 286 GLN cc_start: 0.7905 (tt0) cc_final: 0.7685 (tt0) REVERT: H 80 SER cc_start: 0.7661 (t) cc_final: 0.7295 (p) REVERT: L 9 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.6795 (mp10) REVERT: T 23 PHE cc_start: 0.6060 (m-80) cc_final: 0.5765 (m-80) REVERT: Z 6 GLN cc_start: 0.7621 (mt0) cc_final: 0.7178 (mp10) outliers start: 40 outliers final: 17 residues processed: 226 average time/residue: 0.5024 time to fit residues: 132.0182 Evaluate side-chains 220 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain Z residue 48 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 310 GLN D 186 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN G 303 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094752 restraints weight = 28763.502| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.81 r_work: 0.3099 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.274 22309 Z= 0.246 Angle : 0.619 9.927 30705 Z= 0.290 Chirality : 0.044 0.327 3009 Planarity : 0.005 0.067 3815 Dihedral : 16.012 168.485 4165 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.01 % Favored : 96.81 % Rotamer: Outliers : 2.45 % Allowed : 14.27 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2259 helix: 1.50 (0.14), residues: 1394 sheet: -1.18 (0.85), residues: 42 loop : -0.29 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 311 TYR 0.019 0.002 TYR C 262 PHE 0.025 0.002 PHE G 302 TRP 0.029 0.001 TRP F 19 HIS 0.008 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00573 (22281) covalent geometry : angle 0.61925 (30705) hydrogen bonds : bond 0.04132 ( 1117) hydrogen bonds : angle 4.77044 ( 3183) Misc. bond : bond 0.06267 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8767 (mt-10) REVERT: A 260 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: B 352 ARG cc_start: 0.8412 (mpp80) cc_final: 0.7986 (ptt180) REVERT: C 17 GLU cc_start: 0.8747 (mp0) cc_final: 0.8175 (mp0) REVERT: C 371 ASP cc_start: 0.7716 (t0) cc_final: 0.7164 (t0) REVERT: C 373 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6723 (mm-40) REVERT: C 444 GLU cc_start: 0.7441 (pm20) cc_final: 0.6981 (pm20) REVERT: D 16 ASP cc_start: 0.8679 (m-30) cc_final: 0.8051 (m-30) REVERT: D 20 ASP cc_start: 0.8778 (m-30) cc_final: 0.8423 (m-30) REVERT: D 142 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8159 (t0) REVERT: D 224 GLU cc_start: 0.8212 (tt0) cc_final: 0.7911 (mt-10) REVERT: E 54 GLU cc_start: 0.8911 (pt0) cc_final: 0.8580 (pm20) REVERT: E 74 GLU cc_start: 0.7705 (pt0) cc_final: 0.7431 (mm-30) REVERT: F 42 ILE cc_start: 0.8952 (tt) cc_final: 0.8714 (tt) REVERT: G 206 MET cc_start: 0.8294 (mtm) cc_final: 0.7282 (ttp) REVERT: G 211 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7823 (pp) REVERT: G 225 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7166 (mm-30) REVERT: G 263 LEU cc_start: 0.8643 (tp) cc_final: 0.7983 (tt) REVERT: G 286 GLN cc_start: 0.7935 (tt0) cc_final: 0.7680 (tt0) REVERT: T 23 PHE cc_start: 0.6128 (m-80) cc_final: 0.5794 (m-80) outliers start: 44 outliers final: 18 residues processed: 238 average time/residue: 0.4963 time to fit residues: 137.2441 Evaluate side-chains 223 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 26 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 52 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 159 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN C 370 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN G 195 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098686 restraints weight = 28354.482| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.89 r_work: 0.3147 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.193 22309 Z= 0.128 Angle : 0.543 10.848 30705 Z= 0.257 Chirality : 0.041 0.326 3009 Planarity : 0.004 0.061 3815 Dihedral : 15.643 169.788 4165 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.83 % Favored : 96.99 % Rotamer: Outliers : 1.78 % Allowed : 15.89 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.18), residues: 2259 helix: 1.60 (0.14), residues: 1401 sheet: -0.79 (0.97), residues: 27 loop : -0.29 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 64 TYR 0.016 0.001 TYR C 262 PHE 0.020 0.001 PHE G 302 TRP 0.028 0.001 TRP F 19 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00287 (22281) covalent geometry : angle 0.54308 (30705) hydrogen bonds : bond 0.03810 ( 1117) hydrogen bonds : angle 4.61358 ( 3183) Misc. bond : bond 0.04571 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8721 (mt-10) REVERT: A 260 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.6173 (m-80) REVERT: B 352 ARG cc_start: 0.8416 (mpp80) cc_final: 0.8034 (mpp80) REVERT: C 15 ASP cc_start: 0.6722 (p0) cc_final: 0.6476 (p0) REVERT: C 17 GLU cc_start: 0.8680 (mp0) cc_final: 0.8144 (mp0) REVERT: C 290 TYR cc_start: 0.8719 (m-80) cc_final: 0.8453 (m-80) REVERT: C 371 ASP cc_start: 0.7685 (t0) cc_final: 0.7037 (t0) REVERT: C 444 GLU cc_start: 0.7372 (pm20) cc_final: 0.6897 (pm20) REVERT: D 16 ASP cc_start: 0.8651 (m-30) cc_final: 0.8052 (m-30) REVERT: D 20 ASP cc_start: 0.8751 (m-30) cc_final: 0.8424 (m-30) REVERT: D 142 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8223 (t0) REVERT: D 224 GLU cc_start: 0.8169 (tt0) cc_final: 0.7858 (mt-10) REVERT: F 42 ILE cc_start: 0.8924 (tt) cc_final: 0.8709 (tt) REVERT: G 206 MET cc_start: 0.8133 (mtm) cc_final: 0.7369 (ttp) REVERT: G 211 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7853 (pp) REVERT: G 263 LEU cc_start: 0.8630 (tp) cc_final: 0.7964 (tt) REVERT: G 286 GLN cc_start: 0.7896 (tt0) cc_final: 0.7645 (tt0) REVERT: H 80 SER cc_start: 0.7631 (t) cc_final: 0.7273 (p) REVERT: T 23 PHE cc_start: 0.6163 (m-80) cc_final: 0.5862 (m-80) REVERT: Z 6 GLN cc_start: 0.7596 (mt0) cc_final: 0.7137 (mp-120) outliers start: 32 outliers final: 16 residues processed: 228 average time/residue: 0.5579 time to fit residues: 147.5008 Evaluate side-chains 217 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain Z residue 48 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 186 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 202 optimal weight: 0.0570 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN C 310 GLN G 134 GLN G 195 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099320 restraints weight = 28255.555| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.89 r_work: 0.3159 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.181 22309 Z= 0.127 Angle : 0.541 11.177 30705 Z= 0.257 Chirality : 0.041 0.338 3009 Planarity : 0.004 0.061 3815 Dihedral : 15.464 169.822 4165 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 2.12 % Allowed : 16.05 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.18), residues: 2259 helix: 1.63 (0.14), residues: 1403 sheet: -0.80 (0.97), residues: 27 loop : -0.26 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 64 TYR 0.021 0.001 TYR G 249 PHE 0.018 0.001 PHE G 302 TRP 0.032 0.001 TRP F 19 HIS 0.006 0.001 HIS C 386 Details of bonding type rmsd covalent geometry : bond 0.00285 (22281) covalent geometry : angle 0.54107 (30705) hydrogen bonds : bond 0.03760 ( 1117) hydrogen bonds : angle 4.57490 ( 3183) Misc. bond : bond 0.04296 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8696 (mt-10) REVERT: A 260 PHE cc_start: 0.6562 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: B 352 ARG cc_start: 0.8411 (mpp80) cc_final: 0.8056 (mpp80) REVERT: C 15 ASP cc_start: 0.6579 (p0) cc_final: 0.6369 (p0) REVERT: C 17 GLU cc_start: 0.8689 (mp0) cc_final: 0.8186 (mp0) REVERT: C 290 TYR cc_start: 0.8717 (m-80) cc_final: 0.8414 (m-80) REVERT: C 371 ASP cc_start: 0.7483 (t0) cc_final: 0.7138 (t0) REVERT: C 444 GLU cc_start: 0.7371 (pm20) cc_final: 0.6966 (pm20) REVERT: D 16 ASP cc_start: 0.8659 (m-30) cc_final: 0.8047 (m-30) REVERT: D 20 ASP cc_start: 0.8740 (m-30) cc_final: 0.8382 (m-30) REVERT: D 142 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8286 (t0) REVERT: D 224 GLU cc_start: 0.8169 (tt0) cc_final: 0.7868 (mt-10) REVERT: E 54 GLU cc_start: 0.8794 (pt0) cc_final: 0.8540 (pm20) REVERT: F 42 ILE cc_start: 0.8915 (tt) cc_final: 0.8709 (tt) REVERT: G 206 MET cc_start: 0.8022 (mtm) cc_final: 0.7037 (ttp) REVERT: G 211 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7860 (pp) REVERT: G 219 ILE cc_start: 0.8316 (mm) cc_final: 0.7777 (tt) REVERT: G 225 GLU cc_start: 0.8036 (tp30) cc_final: 0.7202 (mm-30) REVERT: G 263 LEU cc_start: 0.8652 (tp) cc_final: 0.8190 (tt) REVERT: G 286 GLN cc_start: 0.7915 (tt0) cc_final: 0.7658 (tt0) REVERT: H 80 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.7165 (p) REVERT: T 23 PHE cc_start: 0.6186 (m-80) cc_final: 0.5937 (m-80) REVERT: Z 6 GLN cc_start: 0.7551 (mt0) cc_final: 0.7109 (mp-120) outliers start: 38 outliers final: 19 residues processed: 233 average time/residue: 0.4820 time to fit residues: 131.6967 Evaluate side-chains 224 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain Z residue 48 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 111 optimal weight: 0.1980 chunk 48 optimal weight: 0.3980 chunk 213 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 153 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 370 ASN G 171 GLN G 195 GLN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100822 restraints weight = 28084.691| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.89 r_work: 0.3179 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 22309 Z= 0.118 Angle : 0.536 11.187 30705 Z= 0.254 Chirality : 0.040 0.337 3009 Planarity : 0.004 0.061 3815 Dihedral : 15.284 170.534 4165 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.03 % Rotamer: Outliers : 1.51 % Allowed : 16.83 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.18), residues: 2259 helix: 1.68 (0.14), residues: 1405 sheet: -0.76 (0.97), residues: 27 loop : -0.21 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 23 TYR 0.014 0.001 TYR C 262 PHE 0.017 0.001 PHE B 246 TRP 0.035 0.001 TRP F 19 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00260 (22281) covalent geometry : angle 0.53572 (30705) hydrogen bonds : bond 0.03668 ( 1117) hydrogen bonds : angle 4.51037 ( 3183) Misc. bond : bond 0.03774 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8545 (m-80) cc_final: 0.8240 (m-80) REVERT: B 352 ARG cc_start: 0.8432 (mpp80) cc_final: 0.8098 (mpp80) REVERT: C 15 ASP cc_start: 0.6511 (p0) cc_final: 0.6309 (p0) REVERT: C 17 GLU cc_start: 0.8671 (mp0) cc_final: 0.8189 (mp0) REVERT: C 126 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7806 (mt-10) REVERT: C 371 ASP cc_start: 0.7518 (t0) cc_final: 0.7180 (t0) REVERT: C 377 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7856 (tp30) REVERT: C 444 GLU cc_start: 0.7327 (pm20) cc_final: 0.6893 (pm20) REVERT: D 16 ASP cc_start: 0.8661 (m-30) cc_final: 0.7994 (m-30) REVERT: D 20 ASP cc_start: 0.8690 (m-30) cc_final: 0.8366 (m-30) REVERT: D 142 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8279 (t0) REVERT: D 224 GLU cc_start: 0.8149 (tt0) cc_final: 0.7846 (mt-10) REVERT: E 54 GLU cc_start: 0.8766 (pt0) cc_final: 0.8506 (pm20) REVERT: G 206 MET cc_start: 0.7969 (mtm) cc_final: 0.7034 (ttp) REVERT: G 211 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7856 (pp) REVERT: G 219 ILE cc_start: 0.8362 (mm) cc_final: 0.7796 (tt) REVERT: G 225 GLU cc_start: 0.8057 (tp30) cc_final: 0.7195 (mm-30) REVERT: G 263 LEU cc_start: 0.8672 (tp) cc_final: 0.8216 (tt) REVERT: G 286 GLN cc_start: 0.7929 (tt0) cc_final: 0.7657 (tt0) REVERT: H 80 SER cc_start: 0.7318 (t) cc_final: 0.6868 (p) REVERT: T 23 PHE cc_start: 0.6193 (m-80) cc_final: 0.5975 (m-80) REVERT: Z 6 GLN cc_start: 0.7571 (mt0) cc_final: 0.7140 (mp-120) outliers start: 27 outliers final: 16 residues processed: 236 average time/residue: 0.4343 time to fit residues: 120.7972 Evaluate side-chains 221 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 123 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN G 195 GLN L 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097743 restraints weight = 28422.485| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.90 r_work: 0.3142 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 22309 Z= 0.167 Angle : 0.565 9.142 30705 Z= 0.268 Chirality : 0.041 0.261 3009 Planarity : 0.005 0.061 3815 Dihedral : 15.422 171.634 4165 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.03 % Rotamer: Outliers : 1.28 % Allowed : 17.45 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.18), residues: 2259 helix: 1.62 (0.14), residues: 1402 sheet: -0.75 (0.98), residues: 27 loop : -0.27 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 23 TYR 0.024 0.001 TYR G 249 PHE 0.020 0.001 PHE B 246 TRP 0.038 0.001 TRP F 19 HIS 0.006 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00384 (22281) covalent geometry : angle 0.56546 (30705) hydrogen bonds : bond 0.03838 ( 1117) hydrogen bonds : angle 4.59153 ( 3183) Misc. bond : bond 0.04641 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.468 Fit side-chains REVERT: A 260 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: B 352 ARG cc_start: 0.8382 (mpp80) cc_final: 0.8023 (mpp80) REVERT: C 17 GLU cc_start: 0.8689 (mp0) cc_final: 0.8148 (mp0) REVERT: C 371 ASP cc_start: 0.7541 (t0) cc_final: 0.7150 (t0) REVERT: C 377 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7948 (tp30) REVERT: C 444 GLU cc_start: 0.7392 (pm20) cc_final: 0.6971 (pm20) REVERT: D 16 ASP cc_start: 0.8637 (m-30) cc_final: 0.7969 (m-30) REVERT: D 20 ASP cc_start: 0.8700 (m-30) cc_final: 0.8397 (m-30) REVERT: D 142 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8300 (t0) REVERT: D 224 GLU cc_start: 0.8161 (tt0) cc_final: 0.7863 (mt-10) REVERT: E 54 GLU cc_start: 0.8763 (pt0) cc_final: 0.8470 (pm20) REVERT: G 206 MET cc_start: 0.7962 (mtm) cc_final: 0.6965 (ttp) REVERT: G 211 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7864 (pp) REVERT: G 219 ILE cc_start: 0.8360 (mm) cc_final: 0.7855 (tt) REVERT: G 225 GLU cc_start: 0.8073 (tp30) cc_final: 0.7200 (mm-30) REVERT: G 263 LEU cc_start: 0.8655 (tp) cc_final: 0.8179 (tt) REVERT: G 286 GLN cc_start: 0.7935 (tt0) cc_final: 0.7670 (tt0) REVERT: H 80 SER cc_start: 0.7434 (t) cc_final: 0.7009 (p) REVERT: T 23 PHE cc_start: 0.6229 (m-80) cc_final: 0.6015 (m-80) REVERT: Z 6 GLN cc_start: 0.7589 (mt0) cc_final: 0.7124 (mp-120) outliers start: 23 outliers final: 20 residues processed: 215 average time/residue: 0.4747 time to fit residues: 119.2047 Evaluate side-chains 217 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain Z residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 210 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 370 ASN G 171 GLN G 195 GLN L 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099062 restraints weight = 28330.016| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.89 r_work: 0.3153 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 22309 Z= 0.141 Angle : 0.553 10.898 30705 Z= 0.263 Chirality : 0.041 0.258 3009 Planarity : 0.004 0.061 3815 Dihedral : 15.344 173.247 4165 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.74 % Favored : 97.12 % Rotamer: Outliers : 1.39 % Allowed : 17.67 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.18), residues: 2259 helix: 1.63 (0.14), residues: 1405 sheet: -0.77 (0.98), residues: 27 loop : -0.22 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 23 TYR 0.023 0.001 TYR C 290 PHE 0.018 0.001 PHE B 246 TRP 0.037 0.001 TRP F 19 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00322 (22281) covalent geometry : angle 0.55261 (30705) hydrogen bonds : bond 0.03754 ( 1117) hydrogen bonds : angle 4.54919 ( 3183) Misc. bond : bond 0.04318 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5916.47 seconds wall clock time: 102 minutes 4.22 seconds (6124.22 seconds total)