Starting phenix.real_space_refine on Fri Jul 3 08:12:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tj6_25917/07_2026/7tj6_25917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj6_25917/07_2026/7tj6_25917.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/7tj6_25917/07_2026/7tj6_25917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj6_25917/07_2026/7tj6_25917.map" model { file = "/net/cci-nas-00/data/ceres_data/7tj6_25917/07_2026/7tj6_25917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj6_25917/07_2026/7tj6_25917.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tj6_25917/07_2026/7tj6_25917.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tj6_25917/07_2026/7tj6_25917.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 28 5.16 5 C 8616 2.51 5 N 2108 2.21 5 O 2252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13008 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "D" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 101 Unusual residues: {'D21': 5} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 5} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 135 Unusual residues: {'D21': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 5} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 135 Unusual residues: {'D21': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 5} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 5} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 3.27, per 1000 atoms: 0.25 Number of scatterers: 13008 At special positions: 0 Unit cell: (104.796, 104.796, 116.298, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 4 15.00 O 2252 8.00 N 2108 7.00 C 8616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 559.2 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 69.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.565A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 90 through 99 removed outlier: 4.227A pdb=" N LEU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.150A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 159 removed outlier: 3.772A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 removed outlier: 4.033A pdb=" N ALA A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.566A pdb=" N VAL A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 3.702A pdb=" N ALA A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 404 through 418 removed outlier: 4.148A pdb=" N ALA A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.566A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 90 through 99 removed outlier: 4.227A pdb=" N LEU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 127 removed outlier: 4.150A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 159 removed outlier: 3.772A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 159 " --> pdb=" O TRP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 removed outlier: 4.033A pdb=" N ALA B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.566A pdb=" N VAL B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 3.702A pdb=" N ALA B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 404 through 418 removed outlier: 4.148A pdb=" N ALA B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.566A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 90 through 99 removed outlier: 4.227A pdb=" N LEU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 127 removed outlier: 4.150A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 127 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 159 removed outlier: 3.772A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 removed outlier: 4.033A pdb=" N ALA C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.567A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 removed outlier: 3.702A pdb=" N ALA C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'C' and resid 404 through 418 removed outlier: 4.149A pdb=" N ALA C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 48 through 58 removed outlier: 3.565A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 90 through 99 removed outlier: 4.228A pdb=" N LEU D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 127 removed outlier: 4.150A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 159 removed outlier: 3.772A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN D 159 " --> pdb=" O TRP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 removed outlier: 4.033A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.566A pdb=" N VAL D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 299 removed outlier: 3.703A pdb=" N ALA D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 404 through 418 removed outlier: 4.148A pdb=" N ALA D 408 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.717A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.923A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.717A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.923A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.716A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.924A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.716A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.924A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1944 1.30 - 1.43: 3365 1.43 - 1.56: 7871 1.56 - 1.68: 48 1.68 - 1.81: 48 Bond restraints: 13276 Sorted by residual: bond pdb=" C08 D21 D 508 " pdb=" C09 D21 D 508 " ideal model delta sigma weight residual 1.527 1.304 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C08 D21 B 507 " pdb=" C09 D21 B 507 " ideal model delta sigma weight residual 1.527 1.304 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C08 D21 C 507 " pdb=" C09 D21 C 507 " ideal model delta sigma weight residual 1.527 1.305 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C08 D21 A 506 " pdb=" C09 D21 A 506 " ideal model delta sigma weight residual 1.527 1.305 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C09 D21 B 504 " pdb=" C10 D21 B 504 " ideal model delta sigma weight residual 1.526 1.306 0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 13271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.61: 17884 8.61 - 17.21: 32 17.21 - 25.82: 0 25.82 - 34.43: 8 34.43 - 43.03: 24 Bond angle restraints: 17948 Sorted by residual: angle pdb=" C09 D21 C 504 " pdb=" C10 D21 C 504 " pdb=" C11 D21 C 504 " ideal model delta sigma weight residual 112.06 155.09 -43.03 3.00e+00 1.11e-01 2.06e+02 angle pdb=" C09 D21 D 505 " pdb=" C10 D21 D 505 " pdb=" C11 D21 D 505 " ideal model delta sigma weight residual 112.06 155.07 -43.01 3.00e+00 1.11e-01 2.06e+02 angle pdb=" C09 D21 B 504 " pdb=" C10 D21 B 504 " pdb=" C11 D21 B 504 " ideal model delta sigma weight residual 112.06 155.05 -42.99 3.00e+00 1.11e-01 2.05e+02 angle pdb=" C09 D21 A 503 " pdb=" C10 D21 A 503 " pdb=" C11 D21 A 503 " ideal model delta sigma weight residual 112.06 155.04 -42.98 3.00e+00 1.11e-01 2.05e+02 angle pdb=" C07 D21 B 507 " pdb=" C08 D21 B 507 " pdb=" C09 D21 B 507 " ideal model delta sigma weight residual 115.05 157.12 -42.07 3.00e+00 1.11e-01 1.97e+02 ... (remaining 17943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 7784 35.43 - 70.86: 300 70.86 - 106.28: 24 106.28 - 141.71: 12 141.71 - 177.14: 24 Dihedral angle restraints: 8144 sinusoidal: 3544 harmonic: 4600 Sorted by residual: dihedral pdb=" C5' CMP D 502 " pdb=" O5' CMP D 502 " pdb=" P CMP D 502 " pdb=" O1P CMP D 502 " ideal model delta sinusoidal sigma weight residual 60.00 172.83 -112.83 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' CMP C 502 " pdb=" O5' CMP C 502 " pdb=" P CMP C 502 " pdb=" O1P CMP C 502 " ideal model delta sinusoidal sigma weight residual 60.00 172.83 -112.83 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 172.83 -112.83 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 8141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1749 0.096 - 0.191: 283 0.191 - 0.287: 48 0.287 - 0.383: 4 0.383 - 0.479: 8 Chirality restraints: 2092 Sorted by residual: chirality pdb=" C20 D21 A 505 " pdb=" C19 D21 A 505 " pdb=" C21 D21 A 505 " pdb=" O30 D21 A 505 " both_signs ideal model delta sigma weight residual False 2.18 2.65 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" C20 D21 C 506 " pdb=" C19 D21 C 506 " pdb=" C21 D21 C 506 " pdb=" O30 D21 C 506 " both_signs ideal model delta sigma weight residual False 2.18 2.65 -0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" C20 D21 D 507 " pdb=" C19 D21 D 507 " pdb=" C21 D21 D 507 " pdb=" O30 D21 D 507 " both_signs ideal model delta sigma weight residual False 2.18 2.65 -0.48 2.00e-01 2.50e+01 5.68e+00 ... (remaining 2089 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 269 " 0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY C 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY C 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR C 270 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 269 " 0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY D 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY D 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR D 270 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 269 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C GLY A 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY A 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 270 " 0.025 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1123 2.74 - 3.28: 13062 3.28 - 3.82: 20941 3.82 - 4.36: 25568 4.36 - 4.90: 42188 Nonbonded interactions: 102882 Sorted by model distance: nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.198 3.040 nonbonded pdb=" O SER A 220 " pdb=" OG SER A 223 " model vdw 2.302 3.040 nonbonded pdb=" O SER C 220 " pdb=" OG SER C 223 " model vdw 2.302 3.040 nonbonded pdb=" O SER B 220 " pdb=" OG SER B 223 " model vdw 2.302 3.040 nonbonded pdb=" O SER D 220 " pdb=" OG SER D 223 " model vdw 2.303 3.040 ... (remaining 102877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 418 or resid 503 through 504 or (resid 506 and \ (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'B' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'C' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'D' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) } 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: 1.710 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.800 Find NCS groups from input model: 0.260 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 0.223 13276 Z= 0.573 Angle : 2.144 43.031 17948 Z= 0.963 Chirality : 0.075 0.479 2092 Planarity : 0.008 0.080 2176 Dihedral : 20.898 177.140 5176 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.08 % Allowed : 3.35 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1548 helix: 1.16 (0.17), residues: 980 sheet: 0.27 (0.47), residues: 88 loop : -0.72 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 418 TYR 0.023 0.003 TYR D 25 PHE 0.026 0.003 PHE A 309 TRP 0.051 0.005 TRP A 18 HIS 0.006 0.002 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.57 (13276) covalent geometry : angle 2.14423 / 0.96 (17948) hydrogen bonds : bond 0.16793 / 10.93 ( 796) hydrogen bonds : angle 5.89706 / 4.19 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 2 residues processed: 154 average time/residue: 0.5981 time to fit residues: 99.7520 Evaluate side-chains 44 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain D residue 404 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 149 optimal weight: 3.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.086066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.060129 restraints weight = 53353.577| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.13 r_work: 0.3157 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13276 Z= 0.221 Angle : 0.807 9.777 17948 Z= 0.390 Chirality : 0.042 0.142 2092 Planarity : 0.006 0.056 2176 Dihedral : 22.617 166.839 2212 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.60 % Allowed : 9.00 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1548 helix: 1.48 (0.17), residues: 980 sheet: 0.26 (0.49), residues: 88 loop : -0.90 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 343 TYR 0.021 0.002 TYR C 404 PHE 0.012 0.002 PHE D 386 TRP 0.017 0.002 TRP C 18 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (13276) covalent geometry : angle 0.80708 / 0.39 (17948) hydrogen bonds : bond 0.05084 / 3.30 ( 796) hydrogen bonds : angle 4.63348 / 3.26 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 49 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8424 (ptm160) REVERT: B 114 LYS cc_start: 0.9063 (tptt) cc_final: 0.8854 (tppp) REVERT: B 137 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8435 (pp) REVERT: B 255 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8736 (ptm160) REVERT: B 343 ARG cc_start: 0.9198 (mtt180) cc_final: 0.8876 (ppt170) REVERT: C 255 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8610 (ptm160) REVERT: C 303 LYS cc_start: 0.9068 (tppt) cc_final: 0.8848 (tppt) REVERT: D 52 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9213 (pp) REVERT: D 54 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8514 (tp) REVERT: D 392 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7751 (tm) outliers start: 35 outliers final: 9 residues processed: 77 average time/residue: 0.6595 time to fit residues: 54.8941 Evaluate side-chains 47 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 43 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 111 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.083329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057576 restraints weight = 53277.381| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.09 r_work: 0.3124 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13276 Z= 0.179 Angle : 0.713 11.159 17948 Z= 0.340 Chirality : 0.040 0.139 2092 Planarity : 0.005 0.040 2176 Dihedral : 21.462 170.432 2208 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.46 % Allowed : 11.83 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.22), residues: 1548 helix: 1.70 (0.17), residues: 972 sheet: -0.08 (0.51), residues: 96 loop : -0.99 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 343 TYR 0.019 0.002 TYR D 211 PHE 0.009 0.001 PHE C 397 TRP 0.015 0.001 TRP D 18 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (13276) covalent geometry : angle 0.71285 / 0.34 (17948) hydrogen bonds : bond 0.04566 / 2.97 ( 796) hydrogen bonds : angle 4.43456 / 3.08 ( 2304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 41 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 LYS cc_start: 0.9025 (tptt) cc_final: 0.8791 (tppp) REVERT: B 215 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8255 (pp) REVERT: C 114 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8961 (mmmt) REVERT: C 255 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8569 (ptm160) REVERT: C 303 LYS cc_start: 0.9091 (tppt) cc_final: 0.8883 (tppt) REVERT: D 52 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9262 (pp) REVERT: D 392 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7728 (tm) outliers start: 33 outliers final: 3 residues processed: 68 average time/residue: 0.8016 time to fit residues: 58.5393 Evaluate side-chains 41 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 133 optimal weight: 0.0060 chunk 3 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.084031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.058664 restraints weight = 53413.644| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.09 r_work: 0.3153 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13276 Z= 0.132 Angle : 0.676 9.191 17948 Z= 0.319 Chirality : 0.039 0.142 2092 Planarity : 0.005 0.091 2176 Dihedral : 20.173 171.391 2208 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.12 % Allowed : 11.98 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.22), residues: 1548 helix: 1.82 (0.17), residues: 972 sheet: -0.23 (0.51), residues: 96 loop : -0.94 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 343 TYR 0.013 0.001 TYR A 128 PHE 0.013 0.001 PHE D 386 TRP 0.006 0.001 TRP B 18 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (13276) covalent geometry : angle 0.67649 / 0.32 (17948) hydrogen bonds : bond 0.03909 / 2.54 ( 796) hydrogen bonds : angle 4.29894 / 2.99 ( 2304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 37 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 LYS cc_start: 0.9001 (tptt) cc_final: 0.8615 (tptp) REVERT: B 215 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8295 (pp) REVERT: B 386 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8884 (t80) REVERT: C 303 LYS cc_start: 0.9129 (tppt) cc_final: 0.8879 (tppp) REVERT: C 392 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7623 (tm) REVERT: D 22 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8132 (p) REVERT: D 52 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9272 (pp) REVERT: D 392 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7768 (tm) outliers start: 42 outliers final: 5 residues processed: 73 average time/residue: 0.5346 time to fit residues: 43.4141 Evaluate side-chains 45 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 71 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.084155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058767 restraints weight = 53301.270| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.09 r_work: 0.3157 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13276 Z= 0.130 Angle : 0.684 11.476 17948 Z= 0.319 Chirality : 0.039 0.146 2092 Planarity : 0.004 0.046 2176 Dihedral : 18.816 174.613 2208 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.46 % Allowed : 13.24 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.22), residues: 1548 helix: 1.90 (0.17), residues: 972 sheet: -0.21 (0.52), residues: 96 loop : -0.95 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 343 TYR 0.012 0.001 TYR A 128 PHE 0.012 0.001 PHE C 386 TRP 0.006 0.001 TRP B 18 HIS 0.003 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (13276) covalent geometry : angle 0.68386 / 0.32 (17948) hydrogen bonds : bond 0.03721 / 2.42 ( 796) hydrogen bonds : angle 4.28883 / 2.98 ( 2304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 41 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8181 (mm) REVERT: B 114 LYS cc_start: 0.8997 (tptt) cc_final: 0.8621 (tptp) REVERT: B 215 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8290 (pp) REVERT: B 386 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8890 (t80) REVERT: C 255 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8702 (ptm160) REVERT: C 303 LYS cc_start: 0.9114 (tppt) cc_final: 0.8889 (tppp) REVERT: C 392 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7590 (tm) REVERT: D 22 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8146 (p) REVERT: D 52 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9309 (pp) REVERT: D 215 ILE cc_start: 0.8199 (mm) cc_final: 0.7862 (pp) REVERT: D 392 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7922 (tm) outliers start: 33 outliers final: 6 residues processed: 69 average time/residue: 0.5087 time to fit residues: 39.2403 Evaluate side-chains 50 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 0.0060 chunk 103 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 80 optimal weight: 0.0570 chunk 116 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.0118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.083972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.058457 restraints weight = 52373.776| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.10 r_work: 0.3149 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13276 Z= 0.131 Angle : 0.685 10.639 17948 Z= 0.318 Chirality : 0.039 0.154 2092 Planarity : 0.004 0.033 2176 Dihedral : 17.956 177.232 2208 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.53 % Allowed : 13.62 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.22), residues: 1548 helix: 1.93 (0.17), residues: 972 sheet: -0.19 (0.52), residues: 96 loop : -0.95 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 343 TYR 0.022 0.001 TYR B 26 PHE 0.014 0.001 PHE C 397 TRP 0.006 0.001 TRP B 18 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (13276) covalent geometry : angle 0.68503 / 0.32 (17948) hydrogen bonds : bond 0.03675 / 2.40 ( 796) hydrogen bonds : angle 4.21827 / 2.92 ( 2304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 41 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.9196 (mmp) cc_final: 0.8373 (tmt) REVERT: B 114 LYS cc_start: 0.9018 (tptt) cc_final: 0.8636 (tptp) REVERT: B 215 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8289 (pp) REVERT: B 386 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8926 (t80) REVERT: C 255 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8664 (ptm160) REVERT: C 303 LYS cc_start: 0.9126 (tppt) cc_final: 0.8916 (tppp) REVERT: C 369 MET cc_start: 0.7406 (pmm) cc_final: 0.7060 (pmm) REVERT: C 392 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7522 (tm) REVERT: D 22 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8141 (p) REVERT: D 215 ILE cc_start: 0.8366 (mm) cc_final: 0.7987 (pp) REVERT: D 386 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7768 (t80) outliers start: 34 outliers final: 8 residues processed: 71 average time/residue: 0.6114 time to fit residues: 47.8079 Evaluate side-chains 48 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 386 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.082002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.056033 restraints weight = 52909.843| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.05 r_work: 0.3090 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13276 Z= 0.196 Angle : 0.733 13.815 17948 Z= 0.346 Chirality : 0.041 0.172 2092 Planarity : 0.004 0.035 2176 Dihedral : 17.639 176.670 2208 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.79 % Allowed : 15.62 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.22), residues: 1548 helix: 1.73 (0.17), residues: 996 sheet: -0.18 (0.51), residues: 96 loop : -1.16 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 377 TYR 0.025 0.002 TYR B 26 PHE 0.016 0.001 PHE C 397 TRP 0.013 0.001 TRP B 18 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (13276) covalent geometry : angle 0.73337 / 0.35 (17948) hydrogen bonds : bond 0.04264 / 2.78 ( 796) hydrogen bonds : angle 4.27214 / 2.98 ( 2304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.9227 (mmp) cc_final: 0.8327 (tmt) REVERT: B 215 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8249 (pp) REVERT: B 386 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8833 (t80) REVERT: C 215 ILE cc_start: 0.8394 (mm) cc_final: 0.7968 (pp) REVERT: C 255 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8727 (ptm160) REVERT: C 303 LYS cc_start: 0.8983 (tppt) cc_final: 0.8750 (tppp) REVERT: C 369 MET cc_start: 0.7669 (pmm) cc_final: 0.7440 (pmm) REVERT: C 392 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7522 (tm) REVERT: D 215 ILE cc_start: 0.8416 (mm) cc_final: 0.7997 (pp) outliers start: 24 outliers final: 6 residues processed: 61 average time/residue: 0.6190 time to fit residues: 41.5070 Evaluate side-chains 46 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 22 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 105 optimal weight: 0.0770 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.083835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.058446 restraints weight = 52201.037| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.08 r_work: 0.3151 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13276 Z= 0.122 Angle : 0.700 11.746 17948 Z= 0.323 Chirality : 0.039 0.186 2092 Planarity : 0.004 0.032 2176 Dihedral : 16.899 175.646 2208 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.08 % Allowed : 15.48 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.22), residues: 1548 helix: 1.98 (0.17), residues: 972 sheet: -0.21 (0.51), residues: 96 loop : -1.03 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.011 0.001 TYR A 128 PHE 0.015 0.001 PHE C 397 TRP 0.004 0.001 TRP B 18 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13276) covalent geometry : angle 0.69973 / 0.32 (17948) hydrogen bonds : bond 0.03562 / 2.32 ( 796) hydrogen bonds : angle 4.14930 / 2.89 ( 2304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8023 (p) REVERT: A 114 LYS cc_start: 0.8806 (tptp) cc_final: 0.8485 (tptp) REVERT: A 334 MET cc_start: 0.9152 (mmp) cc_final: 0.8367 (tmt) REVERT: B 22 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8018 (p) REVERT: B 114 LYS cc_start: 0.9035 (tptt) cc_final: 0.8569 (tptp) REVERT: B 215 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8151 (pp) REVERT: B 386 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.9070 (t80) REVERT: C 52 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9231 (mm) REVERT: C 215 ILE cc_start: 0.8291 (mm) cc_final: 0.7917 (pp) REVERT: C 255 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8727 (ptm160) REVERT: C 369 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6961 (pmm) REVERT: C 392 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7604 (tm) REVERT: D 22 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8039 (p) REVERT: D 215 ILE cc_start: 0.8325 (mm) cc_final: 0.7946 (pp) outliers start: 28 outliers final: 2 residues processed: 62 average time/residue: 0.6090 time to fit residues: 41.5870 Evaluate side-chains 47 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 22 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.083133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.057510 restraints weight = 52643.970| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.06 r_work: 0.3129 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13276 Z= 0.139 Angle : 0.731 13.112 17948 Z= 0.333 Chirality : 0.039 0.189 2092 Planarity : 0.004 0.034 2176 Dihedral : 16.664 174.268 2208 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.49 % Allowed : 16.15 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1548 helix: 1.97 (0.17), residues: 972 sheet: -0.21 (0.50), residues: 96 loop : -0.99 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.011 0.001 TYR B 26 PHE 0.019 0.001 PHE C 386 TRP 0.008 0.001 TRP B 18 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13276) covalent geometry : angle 0.73076 / 0.33 (17948) hydrogen bonds : bond 0.03683 / 2.40 ( 796) hydrogen bonds : angle 4.12117 / 2.88 ( 2304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8041 (p) REVERT: A 114 LYS cc_start: 0.8800 (tptp) cc_final: 0.8494 (tptp) REVERT: A 334 MET cc_start: 0.9122 (mmp) cc_final: 0.8365 (tmt) REVERT: A 386 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 22 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.8010 (p) REVERT: B 114 LYS cc_start: 0.9011 (tptt) cc_final: 0.8524 (tptp) REVERT: B 215 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8205 (pp) REVERT: C 52 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9253 (mm) REVERT: C 215 ILE cc_start: 0.8323 (mm) cc_final: 0.7915 (pp) REVERT: C 369 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7039 (pmm) REVERT: C 392 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7460 (tm) REVERT: D 22 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8079 (p) REVERT: D 215 ILE cc_start: 0.8345 (mm) cc_final: 0.7935 (pp) outliers start: 20 outliers final: 2 residues processed: 57 average time/residue: 0.6248 time to fit residues: 39.2372 Evaluate side-chains 46 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 124 optimal weight: 0.0170 chunk 110 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 7 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.084130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.058753 restraints weight = 52617.511| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.11 r_work: 0.3163 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13276 Z= 0.124 Angle : 0.734 12.438 17948 Z= 0.333 Chirality : 0.040 0.259 2092 Planarity : 0.004 0.031 2176 Dihedral : 16.357 172.994 2208 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.19 % Allowed : 16.37 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.22), residues: 1548 helix: 2.04 (0.17), residues: 972 sheet: -0.14 (0.51), residues: 96 loop : -0.98 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.011 0.001 TYR A 128 PHE 0.025 0.001 PHE B 386 TRP 0.004 0.000 TRP C 15 HIS 0.002 0.000 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13276) covalent geometry : angle 0.73387 / 0.33 (17948) hydrogen bonds : bond 0.03443 / 2.25 ( 796) hydrogen bonds : angle 4.07451 / 2.84 ( 2304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8076 (p) REVERT: A 114 LYS cc_start: 0.8764 (tptp) cc_final: 0.8447 (tptp) REVERT: A 334 MET cc_start: 0.9082 (mmp) cc_final: 0.8349 (tmt) REVERT: A 386 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 22 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8024 (p) REVERT: B 114 LYS cc_start: 0.9064 (tptt) cc_final: 0.8595 (tptp) REVERT: B 215 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8133 (pp) REVERT: C 52 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9298 (pp) REVERT: C 215 ILE cc_start: 0.8231 (mm) cc_final: 0.7914 (pp) REVERT: C 369 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7101 (pmm) REVERT: C 392 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7652 (tm) REVERT: D 22 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8034 (p) REVERT: D 215 ILE cc_start: 0.8285 (mm) cc_final: 0.7900 (pp) REVERT: D 334 MET cc_start: 0.8875 (mmp) cc_final: 0.7851 (pp-130) outliers start: 16 outliers final: 3 residues processed: 54 average time/residue: 0.4940 time to fit residues: 29.5283 Evaluate side-chains 46 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 47 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 83 optimal weight: 0.0020 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 120 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.083521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.057953 restraints weight = 52488.470| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.06 r_work: 0.3142 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13276 Z= 0.135 Angle : 0.754 14.631 17948 Z= 0.341 Chirality : 0.040 0.252 2092 Planarity : 0.004 0.031 2176 Dihedral : 16.259 172.724 2208 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.19 % Allowed : 16.52 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1548 helix: 1.97 (0.17), residues: 996 sheet: -0.17 (0.51), residues: 96 loop : -1.14 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.010 0.001 TYR A 128 PHE 0.019 0.001 PHE B 386 TRP 0.007 0.001 TRP B 18 HIS 0.001 0.000 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (13276) covalent geometry : angle 0.75357 / 0.34 (17948) hydrogen bonds : bond 0.03547 / 2.31 ( 796) hydrogen bonds : angle 4.08984 / 2.86 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4383.10 seconds wall clock time: 75 minutes 28.51 seconds (4528.51 seconds total)