Starting phenix.real_space_refine on Wed Feb 4 04:17:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p93_71397/02_2026/9p93_71397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p93_71397/02_2026/9p93_71397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p93_71397/02_2026/9p93_71397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p93_71397/02_2026/9p93_71397.map" model { file = "/net/cci-nas-00/data/ceres_data/9p93_71397/02_2026/9p93_71397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p93_71397/02_2026/9p93_71397.cif" } resolution = 3.2 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= 0.040 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 57 5.16 5 C 5425 2.51 5 N 1493 2.21 5 O 1592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8567 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 410 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 233 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "R" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2498 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 12, 'TRANS': 325} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 6, 'TRP:plan': 5, 'ASP:plan': 5, 'HIS:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 196 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1865 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 4 Time building chain proxies: 2.10, per 1000 atoms: 0.25 Number of scatterers: 8567 At special positions: 0 Unit cell: (73.95, 98.6, 168.3, 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 57 16.00 O 1592 8.00 N 1493 7.00 C 5425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 34 " - pdb=" SG CYS R 63 " distance=2.03 Simple disulfide: pdb=" SG CYS R 54 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 77 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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: 0.87 Conformation dependent library (CDL) restraints added in 344.2 milliseconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 42.6% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.784A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.807A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 32 through 36' Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.673A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.879A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.572A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.128A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 Processing helix chain 'R' and resid 27 through 41 removed outlier: 3.891A pdb=" N GLN R 31 " --> pdb=" O PHE R 27 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS R 34 " --> pdb=" O GLU R 30 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU R 35 " --> pdb=" O GLN R 31 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 84 removed outlier: 3.637A pdb=" N PHE R 84 " --> pdb=" O PHE R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 133 Processing helix chain 'R' and resid 144 through 178 Processing helix chain 'R' and resid 183 through 211 Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 264 through 291 removed outlier: 3.946A pdb=" N THR R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.728A pdb=" N VAL R 308 " --> pdb=" O ALA R 304 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 348 through 363 Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 365 through 371 removed outlier: 4.227A pdb=" N PHE R 369 " --> pdb=" O HIS R 365 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE R 371 " --> pdb=" O THR R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 385 Processing helix chain 'R' and resid 388 through 390 No H-bonds generated for 'chain 'R' and resid 388 through 390' Processing helix chain 'R' and resid 391 through 400 Processing helix chain 'R' and resid 404 through 418 Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.704A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.819A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.721A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.708A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.852A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.099A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 62 removed outlier: 4.308A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.753A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.578A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.260A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.911A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.801A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.645A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR N 80 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.512A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 73 through 74 Processing sheet with id=AB2, first strand: chain 'R' and resid 118 through 119 removed outlier: 4.040A pdb=" N GLY R 122 " --> pdb=" O THR R 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.574A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 360 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 289 " --> pdb=" O TYR A 360 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1206 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: 1.35 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2246 1.33 - 1.45: 1682 1.45 - 1.57: 4729 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8735 Sorted by residual: bond pdb=" N VAL R 376 " pdb=" CA VAL R 376 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.22e-02 6.72e+03 8.17e+00 bond pdb=" N VAL P 5 " pdb=" CA VAL P 5 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.76e+00 bond pdb=" N VAL R 203 " pdb=" CA VAL R 203 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.57e+00 bond pdb=" N SER R 372 " pdb=" CA SER R 372 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.17e+00 bond pdb=" N ILE R 309 " pdb=" CA ILE R 309 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.34e-02 5.57e+03 7.07e+00 ... (remaining 8730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11505 1.72 - 3.44: 301 3.44 - 5.16: 24 5.16 - 6.88: 4 6.88 - 8.60: 3 Bond angle restraints: 11837 Sorted by residual: angle pdb=" CA TYR R 157 " pdb=" CB TYR R 157 " pdb=" CG TYR R 157 " ideal model delta sigma weight residual 113.90 120.88 -6.98 1.80e+00 3.09e-01 1.50e+01 angle pdb=" CA VAL R 237 " pdb=" C VAL R 237 " pdb=" O VAL R 237 " ideal model delta sigma weight residual 121.17 117.99 3.18 1.06e+00 8.90e-01 9.00e+00 angle pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" O PRO R 373 " ideal model delta sigma weight residual 121.67 118.05 3.62 1.22e+00 6.72e-01 8.79e+00 angle pdb=" CA VAL R 376 " pdb=" C VAL R 376 " pdb=" O VAL R 376 " ideal model delta sigma weight residual 121.23 118.07 3.16 1.07e+00 8.73e-01 8.71e+00 angle pdb=" CA VAL R 203 " pdb=" C VAL R 203 " pdb=" O VAL R 203 " ideal model delta sigma weight residual 121.17 118.05 3.12 1.06e+00 8.90e-01 8.66e+00 ... (remaining 11832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4750 17.34 - 34.67: 350 34.67 - 52.01: 62 52.01 - 69.34: 11 69.34 - 86.68: 4 Dihedral angle restraints: 5177 sinusoidal: 1960 harmonic: 3217 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 142.94 -49.94 1 1.00e+01 1.00e-02 3.42e+01 dihedral pdb=" CB LYS N 76 " pdb=" CG LYS N 76 " pdb=" CD LYS N 76 " pdb=" CE LYS N 76 " ideal model delta sinusoidal sigma weight residual -60.00 -118.96 58.96 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB CYS R 77 " pdb=" SG CYS R 77 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual -86.00 -61.32 -24.68 1 1.00e+01 1.00e-02 8.77e+00 ... (remaining 5174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 991 0.042 - 0.084: 244 0.084 - 0.126: 92 0.126 - 0.168: 9 0.168 - 0.210: 3 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CA LYS R 378 " pdb=" N LYS R 378 " pdb=" C LYS R 378 " pdb=" CB LYS R 378 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE R 309 " pdb=" N ILE R 309 " pdb=" C ILE R 309 " pdb=" CB ILE R 309 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA LEU P 13 " pdb=" N LEU P 13 " pdb=" C LEU P 13 " pdb=" CB LEU P 13 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1336 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 266 " -0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" C PHE R 266 " 0.091 2.00e-02 2.50e+03 pdb=" O PHE R 266 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR R 267 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 208 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C TRP R 208 " 0.044 2.00e-02 2.50e+03 pdb=" O TRP R 208 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE R 209 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 396 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C VAL R 396 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL R 396 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA R 397 " -0.014 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2064 2.80 - 3.32: 8163 3.32 - 3.85: 13979 3.85 - 4.37: 15914 4.37 - 4.90: 27921 Nonbonded interactions: 68041 Sorted by model distance: nonbonded pdb=" N GLN N 1 " pdb=" OE1 GLN N 1 " model vdw 2.270 3.120 nonbonded pdb=" O PHE R 260 " pdb=" NH1 ARG R 263 " model vdw 2.279 3.120 nonbonded pdb=" O GLN B 9 " pdb=" NE2 GLN B 13 " model vdw 2.312 3.120 nonbonded pdb=" OG1 THR B 86 " pdb=" OE1 GLN A 19 " model vdw 2.324 3.040 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.324 3.120 ... (remaining 68036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.970 Find NCS groups from input model: 0.040 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.003 0.036 8741 Z= 0.211 Angle : 0.601 8.600 11849 Z= 0.383 Chirality : 0.043 0.210 1339 Planarity : 0.004 0.053 1513 Dihedral : 12.548 86.681 3077 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.70 (0.26), residues: 1081 helix: 1.60 (0.26), residues: 424 sheet: 0.31 (0.35), residues: 197 loop : -0.49 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 14 TYR 0.018 0.001 TYR R 157 PHE 0.010 0.001 PHE B 199 TRP 0.020 0.001 TRP R 307 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8735) covalent geometry : angle 0.60046 (11837) SS BOND : bond 0.00223 ( 6) SS BOND : angle 0.91853 ( 12) hydrogen bonds : bond 0.15478 ( 426) hydrogen bonds : angle 5.44066 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.426 Fit side-chains REVERT: B 59 TYR cc_start: 0.8734 (m-80) cc_final: 0.7973 (m-80) REVERT: G 41 CYS cc_start: 0.8505 (m) cc_final: 0.8220 (m) REVERT: N 83 MET cc_start: 0.8791 (mtm) cc_final: 0.8294 (mtm) REVERT: P 17 MET cc_start: 0.8994 (ttm) cc_final: 0.8691 (mtm) REVERT: R 180 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8190 (ttpt) REVERT: R 271 ILE cc_start: 0.8248 (mm) cc_final: 0.7991 (mm) REVERT: R 398 VAL cc_start: 0.8128 (p) cc_final: 0.7808 (m) REVERT: R 406 GLU cc_start: 0.8821 (mp0) cc_final: 0.8438 (mp0) REVERT: A 60 MET cc_start: 0.7452 (mpp) cc_final: 0.7200 (mpp) REVERT: A 205 SER cc_start: 0.6833 (m) cc_final: 0.6371 (t) REVERT: A 343 ASP cc_start: 0.8674 (t70) cc_final: 0.8381 (m-30) REVERT: A 389 ARG cc_start: 0.8365 (ttt180) cc_final: 0.8142 (ttm110) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1222 time to fit residues: 30.2475 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.119204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089207 restraints weight = 18264.728| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.09 r_work: 0.3300 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8741 Z= 0.131 Angle : 0.495 5.806 11849 Z= 0.269 Chirality : 0.040 0.165 1339 Planarity : 0.003 0.030 1513 Dihedral : 3.247 12.501 1198 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.46 % Allowed : 8.43 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.38 (0.25), residues: 1081 helix: 2.52 (0.25), residues: 415 sheet: 0.08 (0.35), residues: 191 loop : -0.14 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 177 TYR 0.028 0.001 TYR R 157 PHE 0.014 0.001 PHE N 68 TRP 0.012 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8735) covalent geometry : angle 0.49451 (11837) SS BOND : bond 0.00099 ( 6) SS BOND : angle 0.51081 ( 12) hydrogen bonds : bond 0.04050 ( 426) hydrogen bonds : angle 4.03248 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8947 (m-80) cc_final: 0.8745 (m-80) REVERT: G 41 CYS cc_start: 0.8517 (m) cc_final: 0.8309 (m) REVERT: N 13 GLN cc_start: 0.5516 (mp10) cc_final: 0.5054 (mp10) REVERT: N 73 ASP cc_start: 0.7104 (p0) cc_final: 0.6893 (p0) REVERT: P 17 MET cc_start: 0.9065 (ttm) cc_final: 0.8814 (mtm) REVERT: R 271 ILE cc_start: 0.8532 (mm) cc_final: 0.8205 (mm) REVERT: R 298 ASP cc_start: 0.8049 (m-30) cc_final: 0.7635 (m-30) REVERT: R 378 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7694 (ttmm) REVERT: R 406 GLU cc_start: 0.8825 (mp0) cc_final: 0.8469 (mp0) REVERT: A 343 ASP cc_start: 0.8683 (t70) cc_final: 0.8472 (m-30) REVERT: A 389 ARG cc_start: 0.8376 (ttt180) cc_final: 0.8091 (mtt90) outliers start: 13 outliers final: 8 residues processed: 139 average time/residue: 0.1063 time to fit residues: 19.8880 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 388 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 21 optimal weight: 0.1980 chunk 58 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 182 HIS R 189 HIS A 12 GLN A 294 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.114627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083787 restraints weight = 18102.338| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.01 r_work: 0.3189 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8741 Z= 0.139 Angle : 0.488 6.591 11849 Z= 0.262 Chirality : 0.040 0.137 1339 Planarity : 0.003 0.040 1513 Dihedral : 3.409 16.282 1198 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.02 % Allowed : 10.90 % Favored : 87.08 % 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: 1.56 (0.25), residues: 1081 helix: 2.72 (0.24), residues: 413 sheet: 0.24 (0.35), residues: 196 loop : -0.11 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 19 TYR 0.022 0.001 TYR R 157 PHE 0.023 0.002 PHE R 260 TRP 0.012 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8735) covalent geometry : angle 0.48750 (11837) SS BOND : bond 0.00097 ( 6) SS BOND : angle 0.56638 ( 12) hydrogen bonds : bond 0.04195 ( 426) hydrogen bonds : angle 3.78003 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.8313 (tmm-80) cc_final: 0.8060 (tmm-80) REVERT: N 13 GLN cc_start: 0.5706 (mp10) cc_final: 0.5212 (mp10) REVERT: N 89 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: R 271 ILE cc_start: 0.8576 (mm) cc_final: 0.8305 (mm) REVERT: R 378 LYS cc_start: 0.8305 (ttpp) cc_final: 0.7821 (ttmm) REVERT: R 399 LEU cc_start: 0.9301 (mt) cc_final: 0.9095 (mp) REVERT: R 406 GLU cc_start: 0.8831 (mp0) cc_final: 0.8489 (mp0) REVERT: A 343 ASP cc_start: 0.8671 (t70) cc_final: 0.8448 (m-30) REVERT: A 358 TYR cc_start: 0.8375 (m-80) cc_final: 0.8022 (m-80) REVERT: A 390 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7637 (mp10) outliers start: 18 outliers final: 14 residues processed: 137 average time/residue: 0.1072 time to fit residues: 19.8791 Evaluate side-chains 134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 390 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.0010 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN P 9 ASN A 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.114106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082660 restraints weight = 18495.272| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.15 r_work: 0.3163 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8741 Z= 0.123 Angle : 0.461 5.587 11849 Z= 0.249 Chirality : 0.039 0.135 1339 Planarity : 0.003 0.041 1513 Dihedral : 3.367 13.386 1198 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.02 % Allowed : 13.26 % Favored : 84.72 % 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: 1.62 (0.25), residues: 1081 helix: 2.84 (0.24), residues: 413 sheet: 0.10 (0.35), residues: 198 loop : -0.06 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 19 TYR 0.020 0.001 TYR R 157 PHE 0.013 0.001 PHE R 233 TRP 0.013 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8735) covalent geometry : angle 0.46143 (11837) SS BOND : bond 0.00089 ( 6) SS BOND : angle 0.43706 ( 12) hydrogen bonds : bond 0.03891 ( 426) hydrogen bonds : angle 3.71612 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.8445 (tmm-80) cc_final: 0.8144 (tmm-80) REVERT: R 181 LEU cc_start: 0.8066 (mt) cc_final: 0.7643 (mt) REVERT: R 271 ILE cc_start: 0.8559 (mm) cc_final: 0.8288 (mm) REVERT: R 378 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7811 (ttmm) REVERT: R 406 GLU cc_start: 0.8885 (mp0) cc_final: 0.8498 (mp0) REVERT: A 343 ASP cc_start: 0.8718 (t70) cc_final: 0.8467 (m-30) outliers start: 18 outliers final: 12 residues processed: 135 average time/residue: 0.0966 time to fit residues: 18.2950 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 81 optimal weight: 0.0970 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.0070 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.115359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084451 restraints weight = 18527.973| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.06 r_work: 0.3203 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8741 Z= 0.095 Angle : 0.445 5.879 11849 Z= 0.240 Chirality : 0.038 0.136 1339 Planarity : 0.003 0.040 1513 Dihedral : 3.253 15.211 1198 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.02 % Allowed : 15.17 % Favored : 82.81 % 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: 1.73 (0.25), residues: 1081 helix: 2.94 (0.25), residues: 413 sheet: 0.20 (0.35), residues: 195 loop : -0.04 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.019 0.001 TYR R 157 PHE 0.024 0.001 PHE R 178 TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 8735) covalent geometry : angle 0.44497 (11837) SS BOND : bond 0.00088 ( 6) SS BOND : angle 0.39136 ( 12) hydrogen bonds : bond 0.03508 ( 426) hydrogen bonds : angle 3.61447 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: B 214 ARG cc_start: 0.8353 (tmm-80) cc_final: 0.8037 (tmm-80) REVERT: N 122 THR cc_start: 0.8407 (p) cc_final: 0.8129 (p) REVERT: R 271 ILE cc_start: 0.8582 (mm) cc_final: 0.8321 (mm) REVERT: R 378 LYS cc_start: 0.8346 (ttpp) cc_final: 0.7908 (ttmm) REVERT: R 406 GLU cc_start: 0.8762 (mp0) cc_final: 0.8497 (mp0) REVERT: A 390 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7625 (mp10) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.0900 time to fit residues: 18.1923 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 403 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 25 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 55 optimal weight: 50.0000 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081439 restraints weight = 18225.535| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.04 r_work: 0.3140 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8741 Z= 0.136 Angle : 0.480 6.151 11849 Z= 0.257 Chirality : 0.039 0.131 1339 Planarity : 0.003 0.042 1513 Dihedral : 3.389 15.050 1198 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.92 % Allowed : 14.83 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.25), residues: 1081 helix: 2.87 (0.25), residues: 419 sheet: 0.19 (0.35), residues: 197 loop : -0.12 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.020 0.001 TYR R 157 PHE 0.017 0.001 PHE R 178 TRP 0.012 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8735) covalent geometry : angle 0.48016 (11837) SS BOND : bond 0.00123 ( 6) SS BOND : angle 0.39293 ( 12) hydrogen bonds : bond 0.03991 ( 426) hydrogen bonds : angle 3.65328 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 42 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8582 (mm-30) REVERT: N 76 LYS cc_start: 0.9271 (mmmt) cc_final: 0.9046 (mttt) REVERT: R 374 GLU cc_start: 0.8074 (pm20) cc_final: 0.7854 (pm20) REVERT: R 378 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7928 (ttmm) REVERT: R 402 PHE cc_start: 0.8779 (m-80) cc_final: 0.8541 (m-80) REVERT: R 404 ASN cc_start: 0.6942 (t0) cc_final: 0.6717 (t0) REVERT: A 390 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7555 (mp10) outliers start: 26 outliers final: 19 residues processed: 139 average time/residue: 0.0952 time to fit residues: 18.5925 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 403 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 50.0000 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.113092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081618 restraints weight = 18439.745| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.14 r_work: 0.3145 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8741 Z= 0.112 Angle : 0.475 8.687 11849 Z= 0.252 Chirality : 0.038 0.153 1339 Planarity : 0.003 0.042 1513 Dihedral : 3.338 14.282 1198 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.58 % Allowed : 15.39 % Favored : 82.02 % 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: 1.66 (0.25), residues: 1081 helix: 2.90 (0.25), residues: 419 sheet: 0.17 (0.34), residues: 209 loop : -0.15 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.019 0.001 TYR R 157 PHE 0.021 0.001 PHE R 260 TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8735) covalent geometry : angle 0.47500 (11837) SS BOND : bond 0.00123 ( 6) SS BOND : angle 0.40079 ( 12) hydrogen bonds : bond 0.03775 ( 426) hydrogen bonds : angle 3.62231 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 42 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8577 (mm-30) REVERT: N 76 LYS cc_start: 0.9288 (mmmt) cc_final: 0.9042 (mttt) REVERT: P 25 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8588 (p) REVERT: R 378 LYS cc_start: 0.8373 (ttpp) cc_final: 0.7909 (ttmm) REVERT: R 402 PHE cc_start: 0.8796 (m-80) cc_final: 0.8570 (m-80) REVERT: A 390 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7683 (mp10) outliers start: 23 outliers final: 17 residues processed: 141 average time/residue: 0.0945 time to fit residues: 18.7312 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 403 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 94 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN R 404 ASN ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.110359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078617 restraints weight = 18374.476| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.10 r_work: 0.3080 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8741 Z= 0.179 Angle : 0.538 9.466 11849 Z= 0.285 Chirality : 0.040 0.152 1339 Planarity : 0.004 0.044 1513 Dihedral : 3.609 15.598 1198 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.58 % Allowed : 15.84 % Favored : 81.57 % 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: 1.61 (0.25), residues: 1081 helix: 2.89 (0.24), residues: 414 sheet: 0.09 (0.34), residues: 216 loop : -0.14 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.021 0.001 TYR R 157 PHE 0.015 0.001 PHE R 233 TRP 0.012 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8735) covalent geometry : angle 0.53815 (11837) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.49308 ( 12) hydrogen bonds : bond 0.04432 ( 426) hydrogen bonds : angle 3.83285 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 42 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8598 (mm-30) REVERT: N 18 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8578 (mp) REVERT: N 68 PHE cc_start: 0.7353 (m-80) cc_final: 0.7124 (m-80) REVERT: N 122 THR cc_start: 0.8477 (p) cc_final: 0.8206 (p) REVERT: P 25 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8520 (p) REVERT: R 378 LYS cc_start: 0.8437 (ttpp) cc_final: 0.7943 (ttmm) REVERT: R 406 GLU cc_start: 0.8860 (mp0) cc_final: 0.8563 (mp0) REVERT: A 390 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7738 (mp10) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.0915 time to fit residues: 17.5544 Evaluate side-chains 137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 403 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.111845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080406 restraints weight = 18391.153| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.12 r_work: 0.3115 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8741 Z= 0.113 Angle : 0.506 10.177 11849 Z= 0.265 Chirality : 0.039 0.167 1339 Planarity : 0.003 0.041 1513 Dihedral : 3.455 14.761 1198 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.70 % Allowed : 15.17 % Favored : 82.13 % 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: 1.67 (0.26), residues: 1081 helix: 2.97 (0.25), residues: 414 sheet: 0.13 (0.34), residues: 216 loop : -0.13 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.019 0.001 TYR R 157 PHE 0.023 0.001 PHE R 260 TRP 0.013 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8735) covalent geometry : angle 0.50654 (11837) SS BOND : bond 0.00126 ( 6) SS BOND : angle 0.42500 ( 12) hydrogen bonds : bond 0.03867 ( 426) hydrogen bonds : angle 3.71325 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 76 LYS cc_start: 0.9330 (mmmt) cc_final: 0.9045 (mttt) REVERT: N 122 THR cc_start: 0.8493 (p) cc_final: 0.8214 (p) REVERT: P 25 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8524 (p) REVERT: R 378 LYS cc_start: 0.8391 (ttpp) cc_final: 0.7939 (ttmm) REVERT: R 406 GLU cc_start: 0.8873 (mp0) cc_final: 0.8561 (mp0) REVERT: A 390 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7700 (mp10) outliers start: 24 outliers final: 17 residues processed: 142 average time/residue: 0.0970 time to fit residues: 19.2573 Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 403 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.112448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081420 restraints weight = 18107.692| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.07 r_work: 0.3134 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8741 Z= 0.113 Angle : 0.517 10.468 11849 Z= 0.268 Chirality : 0.039 0.175 1339 Planarity : 0.003 0.039 1513 Dihedral : 3.440 19.252 1198 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.91 % Allowed : 16.07 % Favored : 82.02 % 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: 1.72 (0.26), residues: 1081 helix: 2.99 (0.25), residues: 414 sheet: 0.14 (0.35), residues: 211 loop : -0.06 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.019 0.001 TYR R 157 PHE 0.016 0.001 PHE N 68 TRP 0.013 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8735) covalent geometry : angle 0.51689 (11837) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.36905 ( 12) hydrogen bonds : bond 0.03716 ( 426) hydrogen bonds : angle 3.67460 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 215 GLU cc_start: 0.8618 (pm20) cc_final: 0.8390 (pm20) REVERT: N 76 LYS cc_start: 0.9313 (mmmt) cc_final: 0.8991 (mttt) REVERT: N 87 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7831 (mttm) REVERT: N 122 THR cc_start: 0.8498 (p) cc_final: 0.8219 (p) REVERT: P 25 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8578 (p) REVERT: R 378 LYS cc_start: 0.8412 (ttpp) cc_final: 0.7947 (ttmm) REVERT: R 406 GLU cc_start: 0.8899 (mp0) cc_final: 0.8645 (mp0) REVERT: A 390 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7708 (mp10) outliers start: 17 outliers final: 15 residues processed: 134 average time/residue: 0.0925 time to fit residues: 17.0550 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 403 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081420 restraints weight = 18364.915| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.09 r_work: 0.3136 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8741 Z= 0.111 Angle : 0.517 10.456 11849 Z= 0.267 Chirality : 0.039 0.170 1339 Planarity : 0.003 0.036 1513 Dihedral : 3.375 18.654 1198 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.13 % Allowed : 15.84 % Favored : 82.02 % 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: 1.79 (0.26), residues: 1081 helix: 2.99 (0.25), residues: 414 sheet: 0.26 (0.35), residues: 207 loop : -0.02 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.019 0.001 TYR P 22 PHE 0.021 0.001 PHE R 260 TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8735) covalent geometry : angle 0.51717 (11837) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.33401 ( 12) hydrogen bonds : bond 0.03625 ( 426) hydrogen bonds : angle 3.64842 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.71 seconds wall clock time: 42 minutes 47.47 seconds (2567.47 seconds total)