Starting phenix.real_space_refine on Fri Feb 14 03:39:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvb_41636/02_2025/8tvb_41636.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvb_41636/02_2025/8tvb_41636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tvb_41636/02_2025/8tvb_41636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvb_41636/02_2025/8tvb_41636.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvb_41636/02_2025/8tvb_41636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvb_41636/02_2025/8tvb_41636.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.152 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6186 2.51 5 N 1605 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9687 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3173 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: C, B Time building chain proxies: 5.78, per 1000 atoms: 0.60 Number of scatterers: 9687 At special positions: 0 Unit cell: (108, 104, 93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1836 8.00 N 1605 7.00 C 6186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 288 " distance=2.04 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS A 451 " - pdb=" SG CYS A 459 " distance=2.02 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 488 " distance=2.19 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 513 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 195 " " NAG A 902 " - " ASN A 169 " " NAG A 903 " - " ASN A 510 " " NAG A 904 " - " ASN A 160 " " NAG B 901 " - " ASN B 195 " " NAG B 902 " - " ASN B 169 " " NAG B 903 " - " ASN B 510 " " NAG B 904 " - " ASN B 160 " " NAG C 901 " - " ASN C 195 " " NAG C 902 " - " ASN C 169 " " NAG C 903 " - " ASN C 510 " " NAG C 904 " - " ASN C 160 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 37.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.878A pdb=" N ILE A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.163A pdb=" N ILE A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.758A pdb=" N GLN A 235 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.668A pdb=" N THR A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.878A pdb=" N ILE B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.163A pdb=" N ILE B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.757A pdb=" N GLN B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 287 through 311 removed outlier: 3.667A pdb=" N THR B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU B 338 " --> pdb=" O ASN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 424 through 427 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.877A pdb=" N ILE C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 4.162A pdb=" N ILE C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.758A pdb=" N GLN C 235 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 287 through 311 removed outlier: 3.668A pdb=" N THR C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 329 through 332 Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 355 Processing helix chain 'C' and resid 424 through 427 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 533 through 537 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429 removed outlier: 7.800A pdb=" N VAL A 434 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU A 141 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS A 436 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS A 143 " --> pdb=" O CYS A 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU A 391 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR A 139 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 389 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU A 141 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA A 387 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS A 143 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N SER A 385 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS A 145 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR A 383 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 411 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 422 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 12.690A pdb=" N SER A 150 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ASN A 266 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP A 152 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE A 268 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 154 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 371 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE A 365 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 373 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 359 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 322 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.545A pdb=" N LEU C 522 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 220 Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508 Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.708A pdb=" N LEU A 522 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 428 through 429 removed outlier: 7.800A pdb=" N VAL B 434 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU B 141 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS B 436 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS B 143 " --> pdb=" O CYS B 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU B 391 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR B 139 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 389 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU B 141 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA B 387 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS B 143 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N SER B 385 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N LYS B 145 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR B 383 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B 411 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 422 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 258 removed outlier: 12.691A pdb=" N SER B 150 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N ASN B 266 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP B 152 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE B 268 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 154 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 371 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 365 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 373 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 359 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 322 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB2, first strand: chain 'B' and resid 506 through 508 Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.708A pdb=" N LEU B 522 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 428 through 429 removed outlier: 7.799A pdb=" N VAL C 434 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU C 141 " --> pdb=" O VAL C 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS C 436 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 143 " --> pdb=" O CYS C 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU C 391 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR C 139 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 389 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU C 141 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA C 387 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS C 143 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N SER C 385 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS C 145 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR C 383 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR C 411 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE C 422 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 258 removed outlier: 12.689A pdb=" N SER C 150 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N ASN C 266 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP C 152 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE C 268 " --> pdb=" O ASP C 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL C 154 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE C 371 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE C 365 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 373 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 359 " --> pdb=" O TYR C 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 322 " --> pdb=" O GLY C 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 397 through 398 413 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1948 1.33 - 1.45: 2051 1.45 - 1.58: 5736 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9825 Sorted by residual: bond pdb=" C5 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C5 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C5 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.40e+00 bond pdb=" C5 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" C5 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.413 1.466 -0.053 2.00e-02 2.50e+03 7.10e+00 ... (remaining 9820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 12064 1.81 - 3.61: 1067 3.61 - 5.42: 135 5.42 - 7.23: 78 7.23 - 9.03: 18 Bond angle restraints: 13362 Sorted by residual: angle pdb=" C TYR C 378 " pdb=" N PRO C 379 " pdb=" CA PRO C 379 " ideal model delta sigma weight residual 119.85 127.73 -7.88 1.01e+00 9.80e-01 6.09e+01 angle pdb=" C TYR B 378 " pdb=" N PRO B 379 " pdb=" CA PRO B 379 " ideal model delta sigma weight residual 119.85 127.72 -7.87 1.01e+00 9.80e-01 6.08e+01 angle pdb=" C TYR A 378 " pdb=" N PRO A 379 " pdb=" CA PRO A 379 " ideal model delta sigma weight residual 119.85 127.70 -7.85 1.01e+00 9.80e-01 6.04e+01 angle pdb=" C THR B 147 " pdb=" N PRO B 148 " pdb=" CA PRO B 148 " ideal model delta sigma weight residual 120.31 127.27 -6.96 9.80e-01 1.04e+00 5.05e+01 angle pdb=" C THR C 147 " pdb=" N PRO C 148 " pdb=" CA PRO C 148 " ideal model delta sigma weight residual 120.31 127.25 -6.94 9.80e-01 1.04e+00 5.02e+01 ... (remaining 13357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5914 17.95 - 35.90: 139 35.90 - 53.86: 34 53.86 - 71.81: 21 71.81 - 89.76: 9 Dihedral angle restraints: 6117 sinusoidal: 2412 harmonic: 3705 Sorted by residual: dihedral pdb=" CA PRO B 148 " pdb=" C PRO B 148 " pdb=" N SER B 149 " pdb=" CA SER B 149 " ideal model delta harmonic sigma weight residual 180.00 161.91 18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO A 148 " pdb=" C PRO A 148 " pdb=" N SER A 149 " pdb=" CA SER A 149 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO C 148 " pdb=" C PRO C 148 " pdb=" N SER C 149 " pdb=" CA SER C 149 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 6114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1218 0.074 - 0.147: 368 0.147 - 0.221: 67 0.221 - 0.294: 3 0.294 - 0.368: 12 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CA CYS A 288 " pdb=" N CYS A 288 " pdb=" C CYS A 288 " pdb=" CB CYS A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA CYS B 288 " pdb=" N CYS B 288 " pdb=" C CYS B 288 " pdb=" CB CYS B 288 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA CYS C 288 " pdb=" N CYS C 288 " pdb=" C CYS C 288 " pdb=" CB CYS C 288 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1665 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 239 " -0.488 9.50e-02 1.11e+02 2.19e-01 2.93e+01 pdb=" NE ARG C 239 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 239 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 239 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 239 " -0.488 9.50e-02 1.11e+02 2.19e-01 2.93e+01 pdb=" NE ARG B 239 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 239 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 239 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 239 " 0.487 9.50e-02 1.11e+02 2.18e-01 2.92e+01 pdb=" NE ARG A 239 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 239 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 239 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 239 " 0.016 2.00e-02 2.50e+03 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 22 2.59 - 3.17: 8117 3.17 - 3.75: 13560 3.75 - 4.32: 21253 4.32 - 4.90: 33280 Nonbonded interactions: 76232 Sorted by model distance: nonbonded pdb=" SG CYS B 451 " pdb=" SG CYS B 459 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS C 451 " pdb=" SG CYS C 459 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS B 427 " pdb=" SG CYS B 436 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 427 " pdb=" SG CYS C 436 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 167 " pdb=" SG CYS B 288 " model vdw 2.041 3.760 ... (remaining 76227 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.280 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.010 0.055 9825 Z= 0.635 Angle : 1.215 9.035 13362 Z= 0.837 Chirality : 0.075 0.368 1668 Planarity : 0.010 0.219 1674 Dihedral : 10.855 89.758 3720 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.20 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1254 helix: -1.65 (0.20), residues: 363 sheet: 0.89 (0.32), residues: 252 loop : 0.56 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.004 TRP C 404 HIS 0.005 0.002 HIS C 438 PHE 0.017 0.003 PHE C 371 TYR 0.032 0.003 TYR C 142 ARG 0.005 0.001 ARG C 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7041 (t0) cc_final: 0.6758 (t0) REVERT: A 509 ASP cc_start: 0.7452 (p0) cc_final: 0.7204 (p0) outliers start: 0 outliers final: 1 residues processed: 217 average time/residue: 1.2962 time to fit residues: 299.7901 Evaluate side-chains 132 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS B 511 GLN C 482 ASN ** C 511 GLN ** 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 = 0.3416 r_free = 0.3416 target = 0.128758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109387 restraints weight = 11175.960| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.77 r_work: 0.3012 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9825 Z= 0.203 Angle : 0.515 7.043 13362 Z= 0.288 Chirality : 0.048 0.185 1668 Planarity : 0.004 0.033 1674 Dihedral : 4.667 29.741 1607 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.39 % Allowed : 8.66 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1254 helix: -0.07 (0.25), residues: 390 sheet: 1.14 (0.29), residues: 294 loop : 0.50 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 404 HIS 0.007 0.001 HIS C 438 PHE 0.015 0.002 PHE B 371 TYR 0.018 0.001 TYR A 468 ARG 0.004 0.001 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.880 Fit side-chains REVERT: A 180 ASP cc_start: 0.8303 (m-30) cc_final: 0.8066 (m-30) REVERT: A 191 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 271 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6847 (mtm) REVERT: A 296 ASP cc_start: 0.8221 (m-30) cc_final: 0.8020 (m-30) REVERT: A 305 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 334 ASN cc_start: 0.7692 (t0) cc_final: 0.7474 (t0) REVERT: A 514 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.8014 (t) REVERT: B 125 HIS cc_start: 0.7698 (t-170) cc_final: 0.6739 (m170) REVERT: B 520 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: C 334 ASN cc_start: 0.8416 (t0) cc_final: 0.7937 (t0) outliers start: 14 outliers final: 2 residues processed: 154 average time/residue: 1.2713 time to fit residues: 209.6677 Evaluate side-chains 120 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 520 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101119 restraints weight = 11443.244| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.79 r_work: 0.2910 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9825 Z= 0.323 Angle : 0.545 4.992 13362 Z= 0.296 Chirality : 0.049 0.166 1668 Planarity : 0.004 0.036 1674 Dihedral : 4.681 26.914 1605 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.07 % Favored : 97.69 % Rotamer: Outliers : 2.59 % Allowed : 9.15 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1254 helix: 0.17 (0.26), residues: 393 sheet: 0.86 (0.31), residues: 258 loop : 0.33 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 404 HIS 0.004 0.001 HIS C 438 PHE 0.019 0.002 PHE C 371 TYR 0.028 0.002 TYR A 468 ARG 0.007 0.001 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.009 Fit side-chains REVERT: A 166 LYS cc_start: 0.7612 (mttt) cc_final: 0.7345 (tttt) REVERT: A 180 ASP cc_start: 0.8616 (m-30) cc_final: 0.8367 (m-30) REVERT: A 181 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7827 (mttt) REVERT: A 191 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 271 MET cc_start: 0.8028 (mmm) cc_final: 0.7322 (mtm) REVERT: A 296 ASP cc_start: 0.8455 (m-30) cc_final: 0.8096 (m-30) REVERT: B 198 LYS cc_start: 0.8240 (pttt) cc_final: 0.8007 (pttp) REVERT: B 511 GLN cc_start: 0.8072 (tp40) cc_final: 0.7737 (mm-40) REVERT: C 166 LYS cc_start: 0.7345 (mmmm) cc_final: 0.6641 (tttp) REVERT: C 305 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: C 509 ASP cc_start: 0.8477 (p0) cc_final: 0.8225 (p0) REVERT: C 511 GLN cc_start: 0.7876 (mt0) cc_final: 0.6939 (mt0) outliers start: 26 outliers final: 6 residues processed: 143 average time/residue: 1.2609 time to fit residues: 193.2911 Evaluate side-chains 109 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 305 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102786 restraints weight = 11376.915| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.79 r_work: 0.2937 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9825 Z= 0.194 Angle : 0.446 5.035 13362 Z= 0.247 Chirality : 0.047 0.153 1668 Planarity : 0.004 0.039 1674 Dihedral : 4.178 23.109 1605 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.91 % Favored : 97.85 % Rotamer: Outliers : 2.09 % Allowed : 11.04 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1254 helix: 0.63 (0.27), residues: 393 sheet: 0.79 (0.31), residues: 258 loop : 0.24 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 404 HIS 0.003 0.001 HIS C 438 PHE 0.012 0.002 PHE C 371 TYR 0.018 0.001 TYR A 468 ARG 0.005 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.196 Fit side-chains REVERT: A 166 LYS cc_start: 0.7673 (mttt) cc_final: 0.7375 (tttt) REVERT: A 180 ASP cc_start: 0.8581 (m-30) cc_final: 0.8342 (m-30) REVERT: A 232 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 271 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7284 (mtm) REVERT: A 296 ASP cc_start: 0.8415 (m-30) cc_final: 0.8047 (m-30) REVERT: B 180 ASP cc_start: 0.8599 (m-30) cc_final: 0.8339 (m-30) REVERT: B 198 LYS cc_start: 0.8186 (pttt) cc_final: 0.7971 (pttp) REVERT: C 166 LYS cc_start: 0.7569 (mmmm) cc_final: 0.6870 (tttp) REVERT: C 520 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: C 527 LYS cc_start: 0.8457 (tttt) cc_final: 0.8224 (ttmm) outliers start: 21 outliers final: 8 residues processed: 124 average time/residue: 1.3583 time to fit residues: 180.1833 Evaluate side-chains 115 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 532 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 272 GLN B 511 GLN ** C 272 GLN ** 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 = 0.3276 r_free = 0.3276 target = 0.118425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.098977 restraints weight = 11461.127| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.76 r_work: 0.2882 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9825 Z= 0.330 Angle : 0.545 6.731 13362 Z= 0.289 Chirality : 0.050 0.155 1668 Planarity : 0.004 0.040 1674 Dihedral : 4.703 40.292 1605 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.47 % Favored : 97.29 % Rotamer: Outliers : 2.29 % Allowed : 11.84 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1254 helix: 0.50 (0.27), residues: 390 sheet: 0.57 (0.31), residues: 258 loop : 0.06 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 404 HIS 0.003 0.001 HIS C 438 PHE 0.019 0.002 PHE C 371 TYR 0.020 0.002 TYR B 468 ARG 0.005 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.164 Fit side-chains REVERT: A 166 LYS cc_start: 0.7695 (mttt) cc_final: 0.7359 (tttt) REVERT: A 180 ASP cc_start: 0.8655 (m-30) cc_final: 0.8425 (m-30) REVERT: A 181 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7785 (mttt) REVERT: A 232 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 251 ASN cc_start: 0.8202 (p0) cc_final: 0.7928 (p0) REVERT: A 271 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7322 (mtm) REVERT: C 166 LYS cc_start: 0.7767 (mmmm) cc_final: 0.7098 (tttp) REVERT: C 282 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7456 (mm-40) REVERT: C 306 ILE cc_start: 0.8314 (pt) cc_final: 0.8085 (pt) REVERT: C 527 LYS cc_start: 0.8475 (tttt) cc_final: 0.8221 (ttmm) outliers start: 23 outliers final: 11 residues processed: 126 average time/residue: 1.1995 time to fit residues: 162.7637 Evaluate side-chains 116 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 532 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100685 restraints weight = 11370.029| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.76 r_work: 0.2901 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9825 Z= 0.280 Angle : 0.498 6.023 13362 Z= 0.268 Chirality : 0.049 0.167 1668 Planarity : 0.004 0.039 1674 Dihedral : 4.593 37.172 1605 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.83 % Favored : 97.93 % Rotamer: Outliers : 2.59 % Allowed : 12.74 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1254 helix: 0.60 (0.27), residues: 393 sheet: 0.53 (0.31), residues: 258 loop : -0.13 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 404 HIS 0.003 0.001 HIS C 438 PHE 0.016 0.002 PHE C 371 TYR 0.021 0.001 TYR B 468 ARG 0.005 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.041 Fit side-chains REVERT: A 166 LYS cc_start: 0.7748 (mttt) cc_final: 0.7334 (tttt) REVERT: A 180 ASP cc_start: 0.8399 (m-30) cc_final: 0.8149 (m-30) REVERT: A 181 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7515 (mttt) REVERT: A 232 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 271 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6949 (mtm) REVERT: A 296 ASP cc_start: 0.8179 (m-30) cc_final: 0.7913 (m-30) REVERT: B 520 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: C 166 LYS cc_start: 0.7805 (mmmm) cc_final: 0.7132 (tttp) REVERT: C 282 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7213 (mm-40) REVERT: C 306 ILE cc_start: 0.8057 (pt) cc_final: 0.7808 (pt) REVERT: C 315 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: C 520 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7333 (mp0) outliers start: 26 outliers final: 10 residues processed: 123 average time/residue: 1.2848 time to fit residues: 169.6195 Evaluate side-chains 113 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 532 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN B 272 GLN B 347 ASN B 511 GLN ** C 272 GLN ** 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 = 0.3287 r_free = 0.3287 target = 0.119628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099504 restraints weight = 11567.045| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.89 r_work: 0.2892 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9825 Z= 0.216 Angle : 0.459 5.541 13362 Z= 0.250 Chirality : 0.047 0.148 1668 Planarity : 0.004 0.038 1674 Dihedral : 4.423 36.196 1605 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.83 % Favored : 97.93 % Rotamer: Outliers : 1.79 % Allowed : 13.73 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1254 helix: 0.80 (0.28), residues: 393 sheet: 0.53 (0.32), residues: 258 loop : -0.18 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 404 HIS 0.002 0.001 HIS C 438 PHE 0.013 0.002 PHE C 371 TYR 0.019 0.001 TYR B 468 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.138 Fit side-chains REVERT: A 166 LYS cc_start: 0.7829 (mttt) cc_final: 0.7449 (tttt) REVERT: A 180 ASP cc_start: 0.8564 (m-30) cc_final: 0.8314 (m-30) REVERT: A 181 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7665 (mttt) REVERT: A 232 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 271 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7173 (mtm) REVERT: A 296 ASP cc_start: 0.8304 (m-30) cc_final: 0.8044 (m-30) REVERT: B 180 ASP cc_start: 0.8564 (m-30) cc_final: 0.8291 (m-30) REVERT: B 520 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: C 166 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7244 (tttp) REVERT: C 282 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7444 (mm-40) REVERT: C 306 ILE cc_start: 0.8253 (pt) cc_final: 0.7991 (pt) REVERT: C 315 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7156 (mp10) outliers start: 18 outliers final: 7 residues processed: 115 average time/residue: 1.2700 time to fit residues: 156.9190 Evaluate side-chains 109 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.098252 restraints weight = 11611.624| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.89 r_work: 0.2870 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9825 Z= 0.270 Angle : 0.493 5.786 13362 Z= 0.265 Chirality : 0.048 0.151 1668 Planarity : 0.004 0.040 1674 Dihedral : 4.520 35.180 1605 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.91 % Favored : 97.85 % Rotamer: Outliers : 1.89 % Allowed : 14.33 % Favored : 83.78 % 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: 0.26 (0.23), residues: 1254 helix: 0.73 (0.28), residues: 393 sheet: 0.49 (0.32), residues: 258 loop : -0.25 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 404 HIS 0.003 0.001 HIS C 438 PHE 0.017 0.002 PHE C 371 TYR 0.023 0.001 TYR B 468 ARG 0.004 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.025 Fit side-chains REVERT: A 166 LYS cc_start: 0.7892 (mttt) cc_final: 0.7538 (tttt) REVERT: A 180 ASP cc_start: 0.8561 (m-30) cc_final: 0.8323 (m-30) REVERT: A 181 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7534 (mtpt) REVERT: A 232 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 271 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7166 (mtm) REVERT: A 296 ASP cc_start: 0.8319 (m-30) cc_final: 0.8057 (m-30) REVERT: A 537 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6164 (pp-130) REVERT: B 180 ASP cc_start: 0.8566 (m-30) cc_final: 0.8316 (m-30) REVERT: B 520 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: C 166 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7377 (tttp) REVERT: C 282 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7474 (mm-40) REVERT: C 306 ILE cc_start: 0.8268 (pt) cc_final: 0.8020 (pt) REVERT: C 315 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7239 (mp10) outliers start: 19 outliers final: 8 residues processed: 111 average time/residue: 1.3061 time to fit residues: 156.3502 Evaluate side-chains 113 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 532 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100886 restraints weight = 11434.897| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.87 r_work: 0.2912 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9825 Z= 0.166 Angle : 0.434 5.289 13362 Z= 0.237 Chirality : 0.047 0.147 1668 Planarity : 0.004 0.041 1674 Dihedral : 4.239 34.054 1605 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.59 % Favored : 98.25 % Rotamer: Outliers : 1.29 % Allowed : 14.93 % Favored : 83.78 % 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: 0.47 (0.24), residues: 1254 helix: 1.04 (0.28), residues: 393 sheet: 0.58 (0.32), residues: 258 loop : -0.21 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 404 HIS 0.002 0.001 HIS C 438 PHE 0.011 0.002 PHE A 331 TYR 0.019 0.001 TYR B 468 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.196 Fit side-chains REVERT: A 166 LYS cc_start: 0.7976 (mttt) cc_final: 0.7637 (tttt) REVERT: A 180 ASP cc_start: 0.8573 (m-30) cc_final: 0.8340 (m-30) REVERT: A 232 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 271 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7140 (mtm) REVERT: A 296 ASP cc_start: 0.8339 (m-30) cc_final: 0.8070 (m-30) REVERT: A 537 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6119 (pp-130) REVERT: B 180 ASP cc_start: 0.8558 (m-30) cc_final: 0.8271 (m-30) REVERT: B 446 TYR cc_start: 0.7112 (t80) cc_final: 0.6901 (t80) REVERT: B 520 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 166 LYS cc_start: 0.7973 (mmmm) cc_final: 0.7407 (tttp) REVERT: C 296 ASP cc_start: 0.8324 (m-30) cc_final: 0.8106 (m-30) REVERT: C 306 ILE cc_start: 0.8210 (pt) cc_final: 0.7969 (pt) REVERT: C 506 MET cc_start: 0.8807 (ttm) cc_final: 0.8598 (mtp) REVERT: C 520 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7401 (mp0) outliers start: 13 outliers final: 3 residues processed: 117 average time/residue: 1.2819 time to fit residues: 161.0351 Evaluate side-chains 110 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 chunk 105 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.101201 restraints weight = 11594.438| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.89 r_work: 0.2922 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9825 Z= 0.166 Angle : 0.437 5.913 13362 Z= 0.237 Chirality : 0.047 0.149 1668 Planarity : 0.004 0.042 1674 Dihedral : 4.157 32.920 1605 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.91 % Favored : 98.01 % Rotamer: Outliers : 0.80 % Allowed : 15.42 % Favored : 83.78 % 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: 0.53 (0.24), residues: 1254 helix: 1.11 (0.28), residues: 393 sheet: 0.61 (0.32), residues: 258 loop : -0.19 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 404 HIS 0.002 0.001 HIS C 438 PHE 0.012 0.002 PHE C 371 TYR 0.021 0.001 TYR B 468 ARG 0.007 0.000 ARG C 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.208 Fit side-chains REVERT: A 166 LYS cc_start: 0.7993 (mttt) cc_final: 0.7707 (tttt) REVERT: A 180 ASP cc_start: 0.8586 (m-30) cc_final: 0.8379 (m-30) REVERT: A 232 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7657 (mm-30) REVERT: A 271 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7222 (mtm) REVERT: A 296 ASP cc_start: 0.8381 (m-30) cc_final: 0.8127 (m-30) REVERT: A 537 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6159 (pp-130) REVERT: B 180 ASP cc_start: 0.8622 (m-30) cc_final: 0.8335 (m-30) REVERT: B 520 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: C 166 LYS cc_start: 0.8039 (mmmm) cc_final: 0.7479 (tttp) REVERT: C 296 ASP cc_start: 0.8375 (m-30) cc_final: 0.8141 (m-30) REVERT: C 306 ILE cc_start: 0.8261 (pt) cc_final: 0.8005 (pt) REVERT: C 520 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7398 (mp0) outliers start: 8 outliers final: 3 residues processed: 114 average time/residue: 1.2384 time to fit residues: 151.9481 Evaluate side-chains 110 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 97 optimal weight: 0.0570 chunk 14 optimal weight: 7.9990 chunk 79 optimal weight: 0.0770 chunk 119 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 511 GLN C 272 GLN C 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105340 restraints weight = 11389.814| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.78 r_work: 0.3032 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9825 Z= 0.124 Angle : 0.410 6.695 13362 Z= 0.224 Chirality : 0.046 0.150 1668 Planarity : 0.004 0.042 1674 Dihedral : 3.936 31.454 1605 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.00 % Allowed : 15.42 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1254 helix: 1.29 (0.28), residues: 393 sheet: 0.71 (0.32), residues: 258 loop : -0.13 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 404 HIS 0.002 0.001 HIS C 231 PHE 0.011 0.001 PHE C 331 TYR 0.019 0.001 TYR B 468 ARG 0.008 0.000 ARG C 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6055.11 seconds wall clock time: 107 minutes 48.52 seconds (6468.52 seconds total)