Starting phenix.real_space_refine on Sat Dec 9 04:14:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/12_2023/6wun_21917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/12_2023/6wun_21917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/12_2023/6wun_21917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/12_2023/6wun_21917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/12_2023/6wun_21917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/12_2023/6wun_21917.pdb" } resolution = 3.9 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= 0.023 sd= 0.112 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 16 5.16 5 C 6370 2.51 5 N 1814 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 394": "OD1" <-> "OD2" Residue "D ASP 436": "OD1" <-> "OD2" Residue "D ARG 482": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2044 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 21, 'TRANS': 238} Chain breaks: 4 Chain: "B" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2997 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Chain: "C" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2044 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 21, 'TRANS': 238} Chain breaks: 4 Chain: "D" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2997 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Time building chain proxies: 5.53, per 1000 atoms: 0.55 Number of scatterers: 10082 At special positions: 0 Unit cell: (149.46, 121.9, 95.4, 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 16 16.00 O 1882 8.00 N 1814 7.00 C 6370 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 - 3.50 Amino acid : False - 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: 4.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 14 sheets defined 28.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.605A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.888A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.939A pdb=" N LEU A 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 removed outlier: 3.799A pdb=" N LEU A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.636A pdb=" N LEU A 182 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.820A pdb=" N ALA A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 255 removed outlier: 3.565A pdb=" N ALA A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.538A pdb=" N ALA A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.670A pdb=" N MET A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.548A pdb=" N ARG A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 removed outlier: 4.585A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 86 through 97 removed outlier: 4.193A pdb=" N ALA B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.766A pdb=" N SER B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.604A pdb=" N ARG C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 82 removed outlier: 4.889A pdb=" N TRP C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.939A pdb=" N LEU C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 removed outlier: 3.799A pdb=" N LEU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 178 through 187 removed outlier: 3.636A pdb=" N LEU C 182 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 210 removed outlier: 3.819A pdb=" N ALA C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 255 removed outlier: 3.566A pdb=" N ALA C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 removed outlier: 3.539A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.671A pdb=" N MET C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.548A pdb=" N ARG C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 71 removed outlier: 4.585A pdb=" N ILE D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 86 through 97 removed outlier: 4.193A pdb=" N ALA D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 458 removed outlier: 3.765A pdb=" N SER D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.341A pdb=" N LEU A 52 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 105 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.643A pdb=" N VAL B 158 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 141 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN B 172 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 159 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 189 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 191 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 197 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AA4, first strand: chain 'B' and resid 293 through 297 removed outlier: 4.031A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.715A pdb=" N ARG B 426 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 417 through 419 removed outlier: 3.575A pdb=" N GLN B 419 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.341A pdb=" N LEU C 52 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 105 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 139 through 141 removed outlier: 3.642A pdb=" N VAL D 158 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D 141 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN D 172 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 159 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 189 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 191 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU D 197 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 206 through 210 Processing sheet with id=AB2, first strand: chain 'D' and resid 293 through 297 removed outlier: 4.031A pdb=" N LEU D 339 " --> pdb=" O ALA D 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 396 through 397 removed outlier: 3.714A pdb=" N ARG D 426 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 417 through 419 removed outlier: 3.576A pdb=" N GLN D 419 " --> pdb=" O GLY D 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 482 through 483 244 hydrogen bonds defined for protein. 672 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: 2.55 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3386 1.34 - 1.46: 1864 1.46 - 1.57: 5020 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 10298 Sorted by residual: bond pdb=" C PHE A 27 " pdb=" N PRO A 28 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.02e+00 bond pdb=" C PHE C 27 " pdb=" N PRO C 28 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" C SER D 255 " pdb=" N PRO D 256 " ideal model delta sigma weight residual 1.331 1.318 0.014 7.90e-03 1.60e+04 2.94e+00 bond pdb=" C SER B 255 " pdb=" N PRO B 256 " ideal model delta sigma weight residual 1.331 1.318 0.013 7.90e-03 1.60e+04 2.90e+00 bond pdb=" CA ALA B 182 " pdb=" C ALA B 182 " ideal model delta sigma weight residual 1.518 1.462 0.056 4.01e-02 6.22e+02 1.92e+00 ... (remaining 10293 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.73: 420 106.73 - 113.55: 5593 113.55 - 120.37: 3839 120.37 - 127.19: 3989 127.19 - 134.01: 143 Bond angle restraints: 13984 Sorted by residual: angle pdb=" N VAL D 258 " pdb=" CA VAL D 258 " pdb=" C VAL D 258 " ideal model delta sigma weight residual 112.98 108.27 4.71 1.25e+00 6.40e-01 1.42e+01 angle pdb=" N VAL B 258 " pdb=" CA VAL B 258 " pdb=" C VAL B 258 " ideal model delta sigma weight residual 112.98 108.27 4.71 1.25e+00 6.40e-01 1.42e+01 angle pdb=" N GLU C 36 " pdb=" CA GLU C 36 " pdb=" C GLU C 36 " ideal model delta sigma weight residual 111.02 115.67 -4.65 1.25e+00 6.40e-01 1.38e+01 angle pdb=" N GLU A 36 " pdb=" CA GLU A 36 " pdb=" C GLU A 36 " ideal model delta sigma weight residual 111.02 115.64 -4.62 1.25e+00 6.40e-01 1.36e+01 angle pdb=" N VAL D 139 " pdb=" CA VAL D 139 " pdb=" C VAL D 139 " ideal model delta sigma weight residual 108.82 105.18 3.64 1.22e+00 6.72e-01 8.88e+00 ... (remaining 13979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5521 17.13 - 34.26: 524 34.26 - 51.39: 79 51.39 - 68.53: 14 68.53 - 85.66: 6 Dihedral angle restraints: 6144 sinusoidal: 2398 harmonic: 3746 Sorted by residual: dihedral pdb=" CA PRO C 34 " pdb=" C PRO C 34 " pdb=" N ASN C 35 " pdb=" CA ASN C 35 " ideal model delta harmonic sigma weight residual -180.00 -148.60 -31.40 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA PRO A 34 " pdb=" C PRO A 34 " pdb=" N ASN A 35 " pdb=" CA ASN A 35 " ideal model delta harmonic sigma weight residual -180.00 -148.62 -31.38 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LEU C 101 " pdb=" C LEU C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta harmonic sigma weight residual -180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1156 0.045 - 0.090: 310 0.090 - 0.135: 90 0.135 - 0.180: 12 0.180 - 0.225: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CB THR A 92 " pdb=" CA THR A 92 " pdb=" OG1 THR A 92 " pdb=" CG2 THR A 92 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR C 92 " pdb=" CA THR C 92 " pdb=" OG1 THR C 92 " pdb=" CG2 THR C 92 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL D 139 " pdb=" N VAL D 139 " pdb=" C VAL D 139 " pdb=" CB VAL D 139 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 1567 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 478 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 479 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 479 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 478 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO B 479 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 189 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 190 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 190 " -0.025 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 644 2.71 - 3.26: 10480 3.26 - 3.81: 14724 3.81 - 4.35: 18561 4.35 - 4.90: 31280 Nonbonded interactions: 75689 Sorted by model distance: nonbonded pdb=" NE2 GLN B 419 " pdb=" OE1 GLU B 484 " model vdw 2.166 2.520 nonbonded pdb=" NE2 GLN D 419 " pdb=" OE1 GLU D 484 " model vdw 2.166 2.520 nonbonded pdb=" O VAL A 283 " pdb=" OG SER A 287 " model vdw 2.176 2.440 nonbonded pdb=" O VAL C 283 " pdb=" OG SER C 287 " model vdw 2.176 2.440 nonbonded pdb=" OG SER B 181 " pdb=" ND2 ASN B 184 " model vdw 2.187 2.520 ... (remaining 75684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 2.460 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.230 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.005 0.056 10298 Z= 0.324 Angle : 0.804 6.441 13984 Z= 0.447 Chirality : 0.046 0.225 1570 Planarity : 0.005 0.057 1828 Dihedral : 13.701 85.657 3740 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.40 % Favored : 81.60 % Rotamer: Outliers : 1.14 % Allowed : 4.36 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -6.35 (0.17), residues: 1288 helix: -3.60 (0.19), residues: 342 sheet: -4.96 (0.21), residues: 320 loop : -4.12 (0.19), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 244 HIS 0.003 0.001 HIS C 178 PHE 0.017 0.002 PHE B 396 TYR 0.014 0.001 TYR D 289 ARG 0.006 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.118 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 143 average time/residue: 0.2267 time to fit residues: 45.2928 Evaluate side-chains 96 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0877 time to fit residues: 2.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10298 Z= 0.219 Angle : 0.716 7.943 13984 Z= 0.356 Chirality : 0.044 0.158 1570 Planarity : 0.005 0.048 1828 Dihedral : 6.287 33.689 1444 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.98 % Favored : 85.02 % Rotamer: Outliers : 0.47 % Allowed : 9.56 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.20), residues: 1288 helix: -1.97 (0.25), residues: 344 sheet: -4.56 (0.22), residues: 300 loop : -3.83 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 168 HIS 0.004 0.001 HIS D 215 PHE 0.018 0.002 PHE D 140 TYR 0.011 0.001 TYR A 240 ARG 0.003 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 0.2017 time to fit residues: 30.8511 Evaluate side-chains 92 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0893 time to fit residues: 2.0364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 0.0070 chunk 40 optimal weight: 0.0980 chunk 96 optimal weight: 10.0000 overall best weight: 1.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10298 Z= 0.194 Angle : 0.670 8.968 13984 Z= 0.332 Chirality : 0.043 0.150 1570 Planarity : 0.004 0.047 1828 Dihedral : 6.035 34.025 1444 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.13 % Favored : 85.87 % Rotamer: Outliers : 1.70 % Allowed : 11.17 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.56 (0.22), residues: 1288 helix: -0.91 (0.29), residues: 332 sheet: -4.31 (0.23), residues: 308 loop : -3.55 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.004 0.001 HIS B 215 PHE 0.026 0.002 PHE A 126 TYR 0.008 0.001 TYR D 351 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.144 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 111 average time/residue: 0.1711 time to fit residues: 29.8923 Evaluate side-chains 99 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0966 time to fit residues: 2.9925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.0030 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 0.0050 chunk 114 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10298 Z= 0.151 Angle : 0.641 10.343 13984 Z= 0.314 Chirality : 0.042 0.148 1570 Planarity : 0.004 0.047 1828 Dihedral : 5.661 34.198 1444 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 1.23 % Allowed : 12.41 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.11 (0.22), residues: 1288 helix: -0.39 (0.29), residues: 332 sheet: -3.95 (0.25), residues: 294 loop : -3.45 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.005 0.001 HIS D 478 PHE 0.024 0.002 PHE C 126 TYR 0.009 0.001 TYR C 240 ARG 0.004 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.143 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 116 average time/residue: 0.1758 time to fit residues: 31.5671 Evaluate side-chains 92 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0896 time to fit residues: 2.3657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 0.0070 chunk 108 optimal weight: 0.0870 chunk 88 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 chunk 42 optimal weight: 6.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10298 Z= 0.151 Angle : 0.647 10.874 13984 Z= 0.313 Chirality : 0.041 0.156 1570 Planarity : 0.004 0.034 1828 Dihedral : 5.428 34.188 1444 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 1.14 % Allowed : 13.54 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.22), residues: 1288 helix: 0.05 (0.30), residues: 330 sheet: -3.66 (0.25), residues: 316 loop : -3.32 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 168 HIS 0.004 0.001 HIS B 215 PHE 0.024 0.002 PHE B 100 TYR 0.009 0.001 TYR D 351 ARG 0.006 0.000 ARG D 494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.142 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 0.1748 time to fit residues: 29.0858 Evaluate side-chains 92 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0942 time to fit residues: 2.4029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10298 Z= 0.166 Angle : 0.639 9.436 13984 Z= 0.308 Chirality : 0.041 0.148 1570 Planarity : 0.004 0.033 1828 Dihedral : 5.388 33.863 1444 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.85 % Allowed : 13.83 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.23), residues: 1288 helix: 0.20 (0.30), residues: 330 sheet: -3.62 (0.25), residues: 306 loop : -3.19 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 168 HIS 0.003 0.001 HIS A 202 PHE 0.020 0.002 PHE C 126 TYR 0.006 0.001 TYR D 183 ARG 0.006 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.066 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 97 average time/residue: 0.1959 time to fit residues: 29.3313 Evaluate side-chains 90 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0916 time to fit residues: 2.9689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN D 64 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10298 Z= 0.227 Angle : 0.670 9.862 13984 Z= 0.324 Chirality : 0.042 0.150 1570 Planarity : 0.004 0.032 1828 Dihedral : 5.566 33.516 1444 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 1.04 % Allowed : 14.58 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.23), residues: 1288 helix: 0.19 (0.30), residues: 330 sheet: -3.67 (0.26), residues: 296 loop : -3.18 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.005 0.001 HIS C 202 PHE 0.026 0.002 PHE B 100 TYR 0.010 0.001 TYR B 289 ARG 0.003 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.112 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 94 average time/residue: 0.1871 time to fit residues: 27.3153 Evaluate side-chains 91 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0936 time to fit residues: 2.7380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10298 Z= 0.234 Angle : 0.677 9.808 13984 Z= 0.328 Chirality : 0.042 0.150 1570 Planarity : 0.004 0.033 1828 Dihedral : 5.654 33.420 1444 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.98 % Favored : 86.02 % Rotamer: Outliers : 0.57 % Allowed : 14.96 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.23), residues: 1288 helix: 0.18 (0.30), residues: 330 sheet: -3.66 (0.26), residues: 298 loop : -3.13 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 168 HIS 0.003 0.001 HIS A 202 PHE 0.026 0.002 PHE D 66 TYR 0.010 0.001 TYR B 289 ARG 0.006 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.109 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 91 average time/residue: 0.1782 time to fit residues: 25.1693 Evaluate side-chains 86 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0888 time to fit residues: 1.7507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 76 optimal weight: 0.0870 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10298 Z= 0.150 Angle : 0.636 9.845 13984 Z= 0.308 Chirality : 0.040 0.149 1570 Planarity : 0.004 0.033 1828 Dihedral : 5.318 33.246 1444 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 16.48 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.23), residues: 1288 helix: 0.31 (0.30), residues: 332 sheet: -3.48 (0.25), residues: 316 loop : -3.00 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 168 HIS 0.004 0.001 HIS B 215 PHE 0.025 0.001 PHE B 100 TYR 0.006 0.001 TYR D 421 ARG 0.004 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1824 time to fit residues: 24.9383 Evaluate side-chains 80 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 0.0040 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 ASN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10298 Z= 0.250 Angle : 0.679 9.973 13984 Z= 0.328 Chirality : 0.042 0.150 1570 Planarity : 0.004 0.033 1828 Dihedral : 5.555 32.921 1444 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.83 % Favored : 85.17 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.23), residues: 1288 helix: 0.29 (0.30), residues: 330 sheet: -3.58 (0.26), residues: 306 loop : -2.99 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 168 HIS 0.004 0.001 HIS B 215 PHE 0.020 0.002 PHE D 66 TYR 0.009 0.001 TYR B 240 ARG 0.005 0.000 ARG A 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2186 time to fit residues: 29.0692 Evaluate side-chains 81 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS C 69 ASN D 192 ASN D 236 HIS ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 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 = 0.3834 r_free = 0.3834 target = 0.144846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130689 restraints weight = 15642.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127276 restraints weight = 31252.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126545 restraints weight = 28655.040| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10298 Z= 0.304 Angle : 0.723 10.322 13984 Z= 0.357 Chirality : 0.043 0.153 1570 Planarity : 0.004 0.036 1828 Dihedral : 5.904 32.794 1444 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.15 % Favored : 83.77 % Rotamer: Outliers : 0.57 % Allowed : 16.86 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.23), residues: 1288 helix: 0.11 (0.30), residues: 332 sheet: -3.92 (0.24), residues: 328 loop : -2.94 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 168 HIS 0.004 0.001 HIS A 202 PHE 0.026 0.002 PHE D 100 TYR 0.012 0.002 TYR B 289 ARG 0.005 0.000 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.54 seconds wall clock time: 33 minutes 36.07 seconds (2016.07 seconds total)