Starting phenix.real_space_refine on Wed Jun 18 15:10:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iiu_60605/06_2025/9iiu_60605_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iiu_60605/06_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_60605/06_2025/9iiu_60605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iiu_60605/06_2025/9iiu_60605.map" model { file = "/net/cci-nas-00/data/ceres_data/9iiu_60605/06_2025/9iiu_60605_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iiu_60605/06_2025/9iiu_60605_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 3} 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: 12.90, per 1000 atoms: 0.60 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: 7.89 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.71 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: 6.76 Time building geometry restraints manager: 8.22 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: 1.390 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: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 48.870 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.550 ------------------------------------------------------------------------------- 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 : 5.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (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 TRP 0.012 0.001 TRP A 131 HIS 0.005 0.001 HIS C 429 PHE 0.020 0.001 PHE B 246 TYR 0.010 0.001 TYR C 262 ARG 0.005 0.000 ARG B 352 Details of bonding type rmsd hydrogen bonds : bond 0.11706 ( 1117) hydrogen bonds : angle 5.75157 ( 3183) covalent geometry : bond 0.00687 (22281) covalent geometry : angle 1.18674 (30705) 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 : 1.860 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: 0.8774 (tt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 1.0684 time to fit residues: 309.3242 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 : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 4.9990 chunk 169 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 0.0070 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 0.0470 chunk 174 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 202 optimal weight: 4.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101960 restraints weight = 28381.634| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.93 r_work: 0.3197 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.306 22309 Z= 0.129 Angle : 0.575 9.177 30705 Z= 0.268 Chirality : 0.042 0.278 3009 Planarity : 0.005 0.064 3815 Dihedral : 16.394 174.475 4165 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.34 % Rotamer: Outliers : 1.23 % Allowed : 7.53 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2259 helix: 1.82 (0.14), residues: 1395 sheet: -0.89 (0.89), residues: 39 loop : -0.10 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 19 HIS 0.012 0.001 HIS A 332 PHE 0.029 0.001 PHE B 246 TYR 0.013 0.001 TYR G 249 ARG 0.005 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 1117) hydrogen bonds : angle 4.87032 ( 3183) covalent geometry : bond 0.00274 (22281) covalent geometry : angle 0.57538 (30705) Misc. bond : bond 0.06834 ( 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 268 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: C 290 TYR cc_start: 0.8789 (m-80) cc_final: 0.8428 (m-80) REVERT: C 444 GLU cc_start: 0.7246 (pm20) cc_final: 0.6919 (pm20) REVERT: D 16 ASP cc_start: 0.8491 (m-30) cc_final: 0.7986 (m-30) REVERT: E 71 ASN cc_start: 0.8163 (t0) cc_final: 0.7851 (t0) REVERT: E 74 GLU cc_start: 0.7766 (pt0) cc_final: 0.7528 (mm-30) REVERT: F 42 ILE cc_start: 0.8858 (tt) cc_final: 0.8645 (tt) REVERT: G 135 ILE cc_start: 0.8597 (tt) cc_final: 0.8388 (pp) REVERT: G 254 TYR cc_start: 0.8180 (t80) cc_final: 0.7757 (t80) REVERT: G 286 GLN cc_start: 0.7903 (tt0) cc_final: 0.7299 (tp40) REVERT: K 15 TYR cc_start: 0.8698 (m-80) cc_final: 0.8485 (m-80) REVERT: T 23 PHE cc_start: 0.5868 (m-80) cc_final: 0.5660 (m-80) REVERT: Z 44 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5472 (mm) outliers start: 22 outliers final: 8 residues processed: 253 average time/residue: 1.0883 time to fit residues: 323.4577 Evaluate side-chains 222 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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 44 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 187 optimal weight: 0.0170 chunk 154 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100451 restraints weight = 28174.450| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.90 r_work: 0.3175 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.244 22309 Z= 0.140 Angle : 0.548 9.205 30705 Z= 0.258 Chirality : 0.042 0.344 3009 Planarity : 0.005 0.063 3815 Dihedral : 15.893 171.423 4165 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.34 % Rotamer: Outliers : 1.84 % Allowed : 11.43 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2259 helix: 1.75 (0.14), residues: 1393 sheet: -0.79 (0.92), residues: 35 loop : -0.14 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 19 HIS 0.012 0.001 HIS A 332 PHE 0.027 0.001 PHE G 302 TYR 0.024 0.001 TYR G 137 ARG 0.006 0.000 ARG H 31 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 1117) hydrogen bonds : angle 4.67777 ( 3183) covalent geometry : bond 0.00316 (22281) covalent geometry : angle 0.54838 (30705) Misc. bond : bond 0.05516 ( 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 259 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: B 350 GLU cc_start: 0.8140 (mp0) cc_final: 0.7767 (mt-10) REVERT: C 444 GLU cc_start: 0.7112 (pm20) cc_final: 0.6763 (pm20) REVERT: D 16 ASP cc_start: 0.8566 (m-30) cc_final: 0.8070 (m-30) REVERT: D 20 ASP cc_start: 0.8597 (m-30) cc_final: 0.8286 (m-30) REVERT: E 54 GLU cc_start: 0.8793 (pt0) cc_final: 0.8477 (pm20) REVERT: E 71 ASN cc_start: 0.8120 (t0) cc_final: 0.7887 (t0) REVERT: F 42 ILE cc_start: 0.8852 (tt) cc_final: 0.8633 (tt) REVERT: G 137 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7799 (t80) REVERT: G 211 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8040 (mm) REVERT: G 225 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7374 (mm-30) REVERT: G 254 TYR cc_start: 0.8241 (t80) cc_final: 0.7800 (t80) REVERT: G 277 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7971 (mtt) REVERT: G 284 TYR cc_start: 0.8142 (m-10) cc_final: 0.7927 (m-10) REVERT: G 286 GLN cc_start: 0.7865 (tt0) cc_final: 0.7294 (tp40) REVERT: K 15 TYR cc_start: 0.8678 (m-80) cc_final: 0.8471 (m-80) REVERT: T 23 PHE cc_start: 0.6006 (m-80) cc_final: 0.5802 (m-80) outliers start: 33 outliers final: 13 residues processed: 241 average time/residue: 1.1075 time to fit residues: 318.4617 Evaluate side-chains 226 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 2.923 ------------------------------------------------------------------------------- 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 15 ASP Chi-restraints excluded: chain C residue 196 VAL 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 211 LEU 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 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 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** 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 = 0.3778 r_free = 0.3778 target = 0.134208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100283 restraints weight = 28585.809| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.91 r_work: 0.3178 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.003 0.224 22309 Z= 0.133 Angle : 0.538 9.271 30705 Z= 0.254 Chirality : 0.041 0.312 3009 Planarity : 0.004 0.062 3815 Dihedral : 15.743 169.506 4165 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.52 % Favored : 97.30 % Rotamer: Outliers : 2.01 % Allowed : 12.71 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2259 helix: 1.76 (0.14), residues: 1394 sheet: -0.87 (0.91), residues: 35 loop : -0.17 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 19 HIS 0.006 0.001 HIS C 120 PHE 0.024 0.001 PHE G 302 TYR 0.019 0.001 TYR G 137 ARG 0.006 0.000 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 1117) hydrogen bonds : angle 4.61213 ( 3183) covalent geometry : bond 0.00300 (22281) covalent geometry : angle 0.53791 (30705) Misc. bond : bond 0.05041 ( 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 254 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8720 (mt-10) REVERT: B 352 ARG cc_start: 0.8386 (mpp80) cc_final: 0.8025 (mpp80) REVERT: C 290 TYR cc_start: 0.8625 (m-80) cc_final: 0.8211 (m-80) REVERT: C 310 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: C 444 GLU cc_start: 0.7103 (pm20) cc_final: 0.6703 (pm20) REVERT: D 16 ASP cc_start: 0.8609 (m-30) cc_final: 0.8051 (m-30) REVERT: D 20 ASP cc_start: 0.8596 (m-30) cc_final: 0.8314 (m-30) REVERT: D 224 GLU cc_start: 0.8123 (tt0) cc_final: 0.7796 (mt-10) REVERT: E 71 ASN cc_start: 0.8122 (t0) cc_final: 0.7914 (t0) REVERT: F 42 ILE cc_start: 0.8836 (tt) cc_final: 0.8618 (tt) REVERT: G 175 GLU cc_start: 0.7885 (tt0) cc_final: 0.7528 (tt0) REVERT: G 206 MET cc_start: 0.7801 (mtm) cc_final: 0.7028 (ttp) REVERT: G 211 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8046 (mm) REVERT: G 225 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7148 (mm-30) REVERT: G 254 TYR cc_start: 0.8231 (t80) cc_final: 0.7778 (t80) REVERT: G 277 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7972 (mtt) REVERT: G 286 GLN cc_start: 0.7915 (tt0) cc_final: 0.7345 (tp40) REVERT: H 80 SER cc_start: 0.7591 (t) cc_final: 0.7217 (p) REVERT: K 15 TYR cc_start: 0.8669 (m-80) cc_final: 0.8465 (m-80) REVERT: T 23 PHE cc_start: 0.6034 (m-80) cc_final: 0.5767 (m-80) outliers start: 36 outliers final: 16 residues processed: 229 average time/residue: 1.0425 time to fit residues: 283.3969 Evaluate side-chains 229 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 313 VAL 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 310 GLN 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 232 MET Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 277 MET 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 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 167 optimal weight: 40.0000 chunk 107 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** 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 = 0.3755 r_free = 0.3755 target = 0.132257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098217 restraints weight = 28548.457| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.90 r_work: 0.3147 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.231 22309 Z= 0.167 Angle : 0.558 9.689 30705 Z= 0.262 Chirality : 0.042 0.318 3009 Planarity : 0.005 0.072 3815 Dihedral : 15.677 167.139 4165 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.66 % Favored : 97.21 % Rotamer: Outliers : 2.23 % Allowed : 12.99 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2259 helix: 1.68 (0.14), residues: 1395 sheet: -0.58 (1.01), residues: 25 loop : -0.22 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 19 HIS 0.006 0.001 HIS C 120 PHE 0.024 0.001 PHE G 302 TYR 0.016 0.001 TYR C 262 ARG 0.010 0.000 ARG C 311 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1117) hydrogen bonds : angle 4.62780 ( 3183) covalent geometry : bond 0.00385 (22281) covalent geometry : angle 0.55814 (30705) Misc. bond : bond 0.05283 ( 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 249 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 1.955 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8754 (mt-10) REVERT: A 260 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.6068 (m-80) REVERT: B 352 ARG cc_start: 0.8422 (mpp80) cc_final: 0.8067 (mpp80) REVERT: C 290 TYR cc_start: 0.8724 (m-80) cc_final: 0.8423 (m-80) REVERT: C 444 GLU cc_start: 0.7175 (pm20) cc_final: 0.6765 (pm20) REVERT: D 16 ASP cc_start: 0.8655 (m-30) cc_final: 0.8065 (m-30) REVERT: D 20 ASP cc_start: 0.8724 (m-30) cc_final: 0.8421 (m-30) REVERT: D 142 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8301 (t0) REVERT: D 224 GLU cc_start: 0.8130 (tt0) cc_final: 0.7810 (mt-10) REVERT: E 54 GLU cc_start: 0.8866 (pt0) cc_final: 0.8502 (pm20) REVERT: E 74 GLU cc_start: 0.7816 (pt0) cc_final: 0.7530 (mm-30) REVERT: F 42 ILE cc_start: 0.8889 (tt) cc_final: 0.8669 (tt) REVERT: G 175 GLU cc_start: 0.7954 (tt0) cc_final: 0.7603 (tt0) REVERT: G 206 MET cc_start: 0.7834 (mtm) cc_final: 0.7060 (ttp) REVERT: G 211 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8056 (mm) REVERT: G 225 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7185 (mm-30) REVERT: G 263 LEU cc_start: 0.8686 (tp) cc_final: 0.8055 (tt) REVERT: G 277 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7894 (mtt) REVERT: G 286 GLN cc_start: 0.7950 (tt0) cc_final: 0.7686 (tt0) REVERT: H 80 SER cc_start: 0.7610 (t) cc_final: 0.7235 (p) REVERT: T 23 PHE cc_start: 0.6100 (m-80) cc_final: 0.5812 (m-80) outliers start: 40 outliers final: 18 residues processed: 226 average time/residue: 1.2191 time to fit residues: 323.2599 Evaluate side-chains 219 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 2.172 ------------------------------------------------------------------------------- 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 313 VAL 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 196 VAL 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 277 MET Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 23 PHE 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 48 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 211 optimal weight: 0.4980 chunk 158 optimal weight: 0.0870 chunk 195 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 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 = 0.3778 r_free = 0.3778 target = 0.134018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100153 restraints weight = 28195.521| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.90 r_work: 0.3168 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.188 22309 Z= 0.132 Angle : 0.531 10.335 30705 Z= 0.251 Chirality : 0.041 0.318 3009 Planarity : 0.004 0.062 3815 Dihedral : 15.450 166.022 4165 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.74 % Favored : 97.12 % Rotamer: Outliers : 1.62 % Allowed : 14.33 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2259 helix: 1.69 (0.14), residues: 1401 sheet: -0.52 (1.01), residues: 25 loop : -0.23 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 19 HIS 0.005 0.001 HIS C 120 PHE 0.022 0.001 PHE G 302 TYR 0.018 0.001 TYR G 249 ARG 0.007 0.000 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1117) hydrogen bonds : angle 4.54636 ( 3183) covalent geometry : bond 0.00297 (22281) covalent geometry : angle 0.53126 (30705) Misc. bond : bond 0.04385 ( 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 250 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 2.372 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8705 (mt-10) REVERT: B 352 ARG cc_start: 0.8428 (mpp80) cc_final: 0.8086 (mpp80) REVERT: C 372 ILE cc_start: 0.8517 (mt) cc_final: 0.8218 (mp) REVERT: C 444 GLU cc_start: 0.7151 (pm20) cc_final: 0.6787 (pm20) REVERT: D 16 ASP cc_start: 0.8608 (m-30) cc_final: 0.8005 (m-30) REVERT: D 20 ASP cc_start: 0.8703 (m-30) cc_final: 0.8384 (m-30) REVERT: D 142 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8246 (t0) REVERT: D 224 GLU cc_start: 0.8123 (tt0) cc_final: 0.7793 (mt-10) REVERT: E 71 ASN cc_start: 0.8225 (t0) cc_final: 0.7979 (t0) REVERT: F 42 ILE cc_start: 0.8887 (tt) cc_final: 0.8673 (tt) REVERT: G 206 MET cc_start: 0.7828 (mtm) cc_final: 0.6906 (ttp) REVERT: G 211 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8014 (mm) REVERT: G 225 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6986 (mm-30) REVERT: G 263 LEU cc_start: 0.8667 (tp) cc_final: 0.8006 (tt) REVERT: G 277 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7831 (mtt) REVERT: G 286 GLN cc_start: 0.7883 (tt0) cc_final: 0.7664 (tt0) REVERT: H 80 SER cc_start: 0.7539 (t) cc_final: 0.7124 (p) REVERT: T 23 PHE cc_start: 0.6119 (m-80) cc_final: 0.5791 (m-80) outliers start: 29 outliers final: 12 residues processed: 231 average time/residue: 1.2167 time to fit residues: 334.1784 Evaluate side-chains 217 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 313 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 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 277 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN D 186 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.132576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098557 restraints weight = 28399.329| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.90 r_work: 0.3145 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 22309 Z= 0.157 Angle : 0.553 10.654 30705 Z= 0.261 Chirality : 0.042 0.332 3009 Planarity : 0.005 0.062 3815 Dihedral : 15.423 164.956 4165 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % Rotamer: Outliers : 2.06 % Allowed : 14.49 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2259 helix: 1.64 (0.14), residues: 1403 sheet: -0.78 (0.97), residues: 27 loop : -0.26 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 19 HIS 0.006 0.001 HIS C 120 PHE 0.020 0.001 PHE B 246 TYR 0.016 0.001 TYR C 262 ARG 0.005 0.000 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 1117) hydrogen bonds : angle 4.57745 ( 3183) covalent geometry : bond 0.00361 (22281) covalent geometry : angle 0.55347 (30705) Misc. bond : bond 0.04683 ( 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 240 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8724 (mt-10) REVERT: A 260 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: B 352 ARG cc_start: 0.8414 (mpp80) cc_final: 0.8068 (mpp80) REVERT: C 290 TYR cc_start: 0.8627 (m-80) cc_final: 0.8303 (m-80) REVERT: C 310 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: C 372 ILE cc_start: 0.8397 (mt) cc_final: 0.8184 (mp) REVERT: C 444 GLU cc_start: 0.7237 (pm20) cc_final: 0.6849 (pm20) REVERT: D 16 ASP cc_start: 0.8628 (m-30) cc_final: 0.7969 (m-30) REVERT: D 20 ASP cc_start: 0.8732 (m-30) cc_final: 0.8424 (m-30) REVERT: D 142 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8290 (t0) REVERT: D 224 GLU cc_start: 0.8154 (tt0) cc_final: 0.7838 (mt-10) REVERT: E 54 GLU cc_start: 0.8855 (pt0) cc_final: 0.8580 (pm20) REVERT: E 71 ASN cc_start: 0.8246 (t0) cc_final: 0.8046 (t0) REVERT: F 42 ILE cc_start: 0.8872 (tt) cc_final: 0.8648 (tt) REVERT: G 206 MET cc_start: 0.7854 (mtm) cc_final: 0.6947 (ttp) REVERT: G 211 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8039 (mm) REVERT: G 225 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7033 (mm-30) REVERT: G 263 LEU cc_start: 0.8680 (tp) cc_final: 0.8028 (tt) REVERT: G 277 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7786 (mtt) REVERT: H 80 SER cc_start: 0.7574 (t) cc_final: 0.7156 (p) REVERT: L 9 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: T 23 PHE cc_start: 0.6122 (m-80) cc_final: 0.5802 (m-80) REVERT: Z 6 GLN cc_start: 0.7602 (mt0) cc_final: 0.7088 (mp-120) outliers start: 37 outliers final: 19 residues processed: 222 average time/residue: 1.0356 time to fit residues: 270.8280 Evaluate side-chains 224 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 313 VAL 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 310 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 272 SER Chi-restraints excluded: chain G residue 277 MET 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 L residue 9 GLN Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain Z residue 15 VAL 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 67 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 222 optimal weight: 0.0870 chunk 184 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 201 optimal weight: 0.0670 chunk 216 optimal weight: 10.0000 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.3776 r_free = 0.3776 target = 0.133904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100034 restraints weight = 28471.927| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.90 r_work: 0.3168 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 22309 Z= 0.126 Angle : 0.540 11.113 30705 Z= 0.255 Chirality : 0.041 0.350 3009 Planarity : 0.004 0.062 3815 Dihedral : 15.294 165.249 4165 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % Rotamer: Outliers : 1.84 % Allowed : 15.50 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2259 helix: 1.68 (0.14), residues: 1402 sheet: -0.79 (0.96), residues: 27 loop : -0.21 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 19 HIS 0.005 0.001 HIS C 120 PHE 0.018 0.001 PHE B 246 TYR 0.019 0.001 TYR G 249 ARG 0.008 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 1117) hydrogen bonds : angle 4.54613 ( 3183) covalent geometry : bond 0.00284 (22281) covalent geometry : angle 0.53986 (30705) Misc. bond : bond 0.04145 ( 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 241 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8712 (mt-10) REVERT: A 260 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.6138 (m-80) REVERT: B 352 ARG cc_start: 0.8414 (mpp80) cc_final: 0.8067 (mpp80) REVERT: B 364 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7232 (mt-10) REVERT: C 290 TYR cc_start: 0.8624 (m-80) cc_final: 0.8272 (m-80) REVERT: C 372 ILE cc_start: 0.8448 (mt) cc_final: 0.8203 (mp) REVERT: C 444 GLU cc_start: 0.7179 (pm20) cc_final: 0.6796 (pm20) REVERT: D 16 ASP cc_start: 0.8659 (m-30) cc_final: 0.8027 (m-30) REVERT: D 20 ASP cc_start: 0.8702 (m-30) cc_final: 0.8387 (m-30) REVERT: D 142 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8296 (t0) REVERT: D 224 GLU cc_start: 0.8121 (tt0) cc_final: 0.7799 (mt-10) REVERT: E 54 GLU cc_start: 0.8808 (pt0) cc_final: 0.8504 (pm20) REVERT: F 42 ILE cc_start: 0.8874 (tt) cc_final: 0.8669 (tt) REVERT: G 206 MET cc_start: 0.7831 (mtm) cc_final: 0.6910 (ttp) REVERT: G 211 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7911 (mm) REVERT: G 219 ILE cc_start: 0.8272 (mm) cc_final: 0.7817 (tt) REVERT: G 225 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7022 (mm-30) REVERT: G 263 LEU cc_start: 0.8670 (tp) cc_final: 0.8238 (tt) REVERT: G 277 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: G 286 GLN cc_start: 0.8132 (tt0) cc_final: 0.7905 (tt0) REVERT: H 80 SER cc_start: 0.7503 (t) cc_final: 0.7073 (p) REVERT: L 9 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6784 (mp10) REVERT: T 23 PHE cc_start: 0.6172 (m-80) cc_final: 0.5845 (m-80) REVERT: Z 6 GLN cc_start: 0.7601 (mt0) cc_final: 0.7103 (mp10) outliers start: 33 outliers final: 19 residues processed: 225 average time/residue: 1.0384 time to fit residues: 275.2686 Evaluate side-chains 221 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 LEU 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 142 ASN 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 277 MET 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 15 VAL 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 222 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN G 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094210 restraints weight = 28670.993| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.88 r_work: 0.3095 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.256 22309 Z= 0.268 Angle : 0.648 11.080 30705 Z= 0.302 Chirality : 0.045 0.364 3009 Planarity : 0.005 0.062 3815 Dihedral : 15.856 167.569 4165 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.97 % Favored : 96.90 % Rotamer: Outliers : 1.90 % Allowed : 15.33 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2259 helix: 1.48 (0.14), residues: 1393 sheet: -1.06 (0.94), residues: 32 loop : -0.29 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 19 HIS 0.009 0.002 HIS C 120 PHE 0.023 0.002 PHE B 246 TYR 0.023 0.002 TYR C 262 ARG 0.008 0.001 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 1117) hydrogen bonds : angle 4.79080 ( 3183) covalent geometry : bond 0.00625 (22281) covalent geometry : angle 0.64777 (30705) Misc. bond : bond 0.06080 ( 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 236 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 2.011 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8742 (mt-10) REVERT: A 260 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6227 (m-80) REVERT: B 352 ARG cc_start: 0.8375 (mpp80) cc_final: 0.8006 (mpp80) REVERT: C 444 GLU cc_start: 0.7478 (pm20) cc_final: 0.6976 (pm20) REVERT: D 16 ASP cc_start: 0.8684 (m-30) cc_final: 0.8020 (m-30) REVERT: D 20 ASP cc_start: 0.8747 (m-30) cc_final: 0.8415 (m-30) REVERT: D 142 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8160 (t0) REVERT: D 224 GLU cc_start: 0.8218 (tt0) cc_final: 0.7917 (mt-10) REVERT: E 74 GLU cc_start: 0.7693 (pt0) cc_final: 0.7431 (mm-30) REVERT: F 42 ILE cc_start: 0.8962 (tt) cc_final: 0.8733 (tt) REVERT: G 206 MET cc_start: 0.7945 (mtm) cc_final: 0.7066 (ttp) REVERT: G 211 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7969 (mm) REVERT: G 219 ILE cc_start: 0.8451 (mm) cc_final: 0.7830 (tt) REVERT: G 225 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7179 (mm-30) REVERT: G 262 MET cc_start: 0.6517 (ptt) cc_final: 0.6276 (ptp) REVERT: G 263 LEU cc_start: 0.8721 (tp) cc_final: 0.8268 (tt) REVERT: H 80 SER cc_start: 0.7700 (t) cc_final: 0.7339 (p) REVERT: T 23 PHE cc_start: 0.6173 (m-80) cc_final: 0.5852 (m-80) REVERT: Z 6 GLN cc_start: 0.7686 (mt0) cc_final: 0.7454 (mt0) outliers start: 34 outliers final: 19 residues processed: 219 average time/residue: 1.2931 time to fit residues: 340.7016 Evaluate side-chains 215 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 313 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 398 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 142 ASN 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 H residue 77 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 6 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 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 = 0.3761 r_free = 0.3761 target = 0.132566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098692 restraints weight = 28449.464| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.89 r_work: 0.3150 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 22309 Z= 0.135 Angle : 0.555 9.408 30705 Z= 0.263 Chirality : 0.041 0.265 3009 Planarity : 0.004 0.061 3815 Dihedral : 15.508 171.142 4165 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.79 % Favored : 97.08 % Rotamer: Outliers : 1.51 % Allowed : 16.39 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2259 helix: 1.58 (0.14), residues: 1401 sheet: -0.75 (0.98), residues: 27 loop : -0.29 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 19 HIS 0.006 0.001 HIS A 332 PHE 0.018 0.001 PHE B 246 TYR 0.022 0.001 TYR C 290 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1117) hydrogen bonds : angle 4.61260 ( 3183) covalent geometry : bond 0.00307 (22281) covalent geometry : angle 0.55469 (30705) Misc. bond : bond 0.04394 ( 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 234 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 1.889 Fit side-chains REVERT: A 132 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8711 (mt-10) REVERT: A 260 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: B 352 ARG cc_start: 0.8412 (mpp80) cc_final: 0.8029 (mpp80) REVERT: C 370 ASN cc_start: 0.8062 (m-40) cc_final: 0.7700 (m-40) REVERT: C 377 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7937 (tp30) REVERT: C 444 GLU cc_start: 0.7393 (pm20) cc_final: 0.6904 (pm20) REVERT: D 16 ASP cc_start: 0.8655 (m-30) cc_final: 0.7988 (m-30) REVERT: D 20 ASP cc_start: 0.8728 (m-30) cc_final: 0.8421 (m-30) REVERT: D 142 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8229 (t0) REVERT: D 224 GLU cc_start: 0.8163 (tt0) cc_final: 0.7858 (mt-10) REVERT: E 54 GLU cc_start: 0.8764 (pt0) cc_final: 0.8522 (pm20) REVERT: F 42 ILE cc_start: 0.8910 (tt) cc_final: 0.8708 (tt) REVERT: G 175 GLU cc_start: 0.7922 (tt0) cc_final: 0.7394 (tt0) REVERT: G 206 MET cc_start: 0.7881 (mtm) cc_final: 0.6889 (ttp) REVERT: G 211 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7895 (mm) REVERT: G 219 ILE cc_start: 0.8323 (mm) cc_final: 0.7874 (tt) REVERT: G 225 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7045 (mm-30) REVERT: G 263 LEU cc_start: 0.8681 (tp) cc_final: 0.8250 (tt) REVERT: G 284 TYR cc_start: 0.8098 (m-10) cc_final: 0.7879 (m-10) REVERT: H 80 SER cc_start: 0.7527 (t) cc_final: 0.7162 (p) REVERT: T 23 PHE cc_start: 0.6246 (m-80) cc_final: 0.5915 (m-80) REVERT: Z 6 GLN cc_start: 0.7588 (mt0) cc_final: 0.7046 (mp-120) outliers start: 27 outliers final: 16 residues processed: 221 average time/residue: 1.1163 time to fit residues: 289.0181 Evaluate side-chains 215 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 2.068 ------------------------------------------------------------------------------- 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 313 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 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 H residue 77 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain Z residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 127 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 137 optimal weight: 0.0980 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 50.0000 chunk 83 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3754 r_free = 0.3754 target = 0.132183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098112 restraints weight = 28374.841| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.91 r_work: 0.3147 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 22309 Z= 0.141 Angle : 0.563 11.417 30705 Z= 0.265 Chirality : 0.041 0.315 3009 Planarity : 0.004 0.061 3815 Dihedral : 15.423 172.923 4165 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % Rotamer: Outliers : 1.23 % Allowed : 16.89 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2259 helix: 1.58 (0.14), residues: 1404 sheet: -0.71 (0.98), residues: 27 loop : -0.25 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 19 HIS 0.007 0.001 HIS A 332 PHE 0.018 0.001 PHE B 246 TYR 0.023 0.001 TYR C 290 ARG 0.007 0.000 ARG B 422 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 1117) hydrogen bonds : angle 4.57487 ( 3183) covalent geometry : bond 0.00321 (22281) covalent geometry : angle 0.56323 (30705) Misc. bond : bond 0.04336 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13602.83 seconds wall clock time: 236 minutes 15.25 seconds (14175.25 seconds total)