Starting phenix.real_space_refine on Wed Mar 4 04:30:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x19_21993/03_2026/6x19_21993.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x19_21993/03_2026/6x19_21993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x19_21993/03_2026/6x19_21993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x19_21993/03_2026/6x19_21993.map" model { file = "/net/cci-nas-00/data/ceres_data/6x19_21993/03_2026/6x19_21993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x19_21993/03_2026/6x19_21993.cif" } resolution = 2.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 843 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 6462 2.51 5 N 1748 2.21 5 O 2003 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10277 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2876 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: "R" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3203 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain breaks: 2 Chain: "R" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'UK1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 2.01, per 1000 atoms: 0.20 Number of scatterers: 10277 At special positions: 0 Unit cell: (115.37, 96.28, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 F 2 9.00 O 2003 8.00 N 1748 7.00 C 6462 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=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.01 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.05 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.01 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: 0.81 Conformation dependent library (CDL) restraints added in 480.2 milliseconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 46.4% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 91 through 112 Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.053A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.848A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.728A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.548A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 31 through 53 removed outlier: 4.029A pdb=" N GLN R 37 " --> pdb=" O TRP R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 117 removed outlier: 3.820A pdb=" N SER R 117 " --> pdb=" O ASP R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 127 removed outlier: 3.724A pdb=" N GLU R 127 " --> pdb=" O SER R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 141 through 167 Processing helix chain 'R' and resid 169 through 173 Processing helix chain 'R' and resid 174 through 208 Processing helix chain 'R' and resid 210 through 212 No H-bonds generated for 'chain 'R' and resid 210 through 212' Processing helix chain 'R' and resid 213 through 223 removed outlier: 3.626A pdb=" N LEU R 217 " --> pdb=" O GLN R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.956A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 removed outlier: 3.698A pdb=" N PHE R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 292 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 341 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 369 Processing helix chain 'R' and resid 379 through 393 removed outlier: 3.691A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 403 Processing helix chain 'R' and resid 406 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.292A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.159A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.562A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.764A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.542A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.738A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.687A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.649A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.939A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.550A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 80 through 83 525 hydrogen bonds defined for protein. 1485 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: 1.61 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1661 1.32 - 1.44: 2925 1.44 - 1.57: 5697 1.57 - 1.69: 11 1.69 - 1.82: 85 Bond restraints: 10379 Sorted by residual: bond pdb=" C03 UK1 R 501 " pdb=" N07 UK1 R 501 " ideal model delta sigma weight residual 1.423 1.722 -0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C46 UK1 R 501 " pdb=" N43 UK1 R 501 " ideal model delta sigma weight residual 1.419 1.628 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C31 UK1 R 501 " pdb=" N33 UK1 R 501 " ideal model delta sigma weight residual 1.413 1.605 -0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" C57 UK1 R 501 " pdb=" C58 UK1 R 501 " ideal model delta sigma weight residual 1.620 1.435 0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" C28 UK1 R 501 " pdb=" C60 UK1 R 501 " ideal model delta sigma weight residual 1.521 1.674 -0.153 2.00e-02 2.50e+03 5.83e+01 ... (remaining 10374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.01: 14072 8.01 - 16.01: 12 16.01 - 24.02: 1 24.02 - 32.03: 0 32.03 - 40.03: 1 Bond angle restraints: 14086 Sorted by residual: angle pdb=" C28 UK1 R 501 " pdb=" C57 UK1 R 501 " pdb=" C58 UK1 R 501 " ideal model delta sigma weight residual 110.03 70.00 40.03 3.00e+00 1.11e-01 1.78e+02 angle pdb=" N PRO A 115 " pdb=" CA PRO A 115 " pdb=" C PRO A 115 " ideal model delta sigma weight residual 110.70 99.23 11.47 1.22e+00 6.72e-01 8.83e+01 angle pdb=" C PHE A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta sigma weight residual 119.66 125.30 -5.64 7.30e-01 1.88e+00 5.96e+01 angle pdb=" N ASN A 14 " pdb=" CA ASN A 14 " pdb=" C ASN A 14 " ideal model delta sigma weight residual 113.41 105.34 8.07 1.22e+00 6.72e-01 4.37e+01 angle pdb=" N GLN A 19 " pdb=" CA GLN A 19 " pdb=" C GLN A 19 " ideal model delta sigma weight residual 113.23 105.99 7.24 1.24e+00 6.50e-01 3.41e+01 ... (remaining 14081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5619 17.78 - 35.56: 467 35.56 - 53.34: 69 53.34 - 71.12: 25 71.12 - 88.89: 10 Dihedral angle restraints: 6190 sinusoidal: 2505 harmonic: 3685 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C ASN A 371 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " pdb=" CB ASN A 371 " ideal model delta harmonic sigma weight residual -122.60 -135.35 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ARG A 317 " pdb=" N ARG A 317 " pdb=" CA ARG A 317 " pdb=" CB ARG A 317 " ideal model delta harmonic sigma weight residual -122.60 -110.51 -12.09 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 6187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1274 0.090 - 0.179: 202 0.179 - 0.269: 45 0.269 - 0.358: 17 0.358 - 0.448: 4 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ASP R 293 " pdb=" N ASP R 293 " pdb=" C ASP R 293 " pdb=" CB ASP R 293 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA ASN A 371 " pdb=" N ASN A 371 " pdb=" C ASN A 371 " pdb=" CB ASN A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA GLU R 125 " pdb=" N GLU R 125 " pdb=" C GLU R 125 " pdb=" CB GLU R 125 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 1539 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 290 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C LEU R 290 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU R 290 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR R 291 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 101 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C TYR R 101 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR R 101 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG R 102 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 155 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C GLU A 155 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU A 155 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 156 " -0.015 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 299 2.69 - 3.24: 10501 3.24 - 3.79: 16930 3.79 - 4.35: 24127 4.35 - 4.90: 37142 Nonbonded interactions: 88999 Sorted by model distance: nonbonded pdb=" OH TYR B 105 " pdb=" O HOH B 401 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASP A 141 " pdb=" CD PRO A 143 " model vdw 2.158 3.440 nonbonded pdb=" OE1 GLU A 392 " pdb=" O HOH A 401 " model vdw 2.185 3.040 nonbonded pdb=" OE2 GLU A 209 " pdb=" O HOH A 402 " model vdw 2.244 3.040 nonbonded pdb=" N GLU A 145 " pdb=" OE1 GLU A 145 " model vdw 2.269 3.120 ... (remaining 88994 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=0.00 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.760 Find NCS groups from input model: 0.060 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:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.299 10385 Z= 0.604 Angle : 1.150 40.033 14098 Z= 0.768 Chirality : 0.078 0.448 1542 Planarity : 0.005 0.047 1793 Dihedral : 13.948 88.894 3786 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.26 % Rotamer: Outliers : 1.01 % Allowed : 4.04 % Favored : 94.95 % Cbeta Deviations : 0.50 % 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 (0.22), residues: 1240 helix: -1.26 (0.20), residues: 519 sheet: -0.58 (0.31), residues: 241 loop : -0.83 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 170 TYR 0.030 0.002 TYR B 59 PHE 0.018 0.002 PHE A 363 TRP 0.024 0.002 TRP R 87 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00984 (10379) covalent geometry : angle 1.14672 (14086) SS BOND : bond 0.01505 ( 6) SS BOND : angle 3.12622 ( 12) hydrogen bonds : bond 0.23772 ( 525) hydrogen bonds : angle 8.54453 ( 1485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.8032 (pt0) cc_final: 0.7744 (pt0) REVERT: A 344 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7435 (mm-30) REVERT: R 117 SER cc_start: 0.2598 (OUTLIER) cc_final: 0.1520 (t) REVERT: R 267 ARG cc_start: 0.6435 (mmt180) cc_final: 0.6220 (tpt170) outliers start: 11 outliers final: 1 residues processed: 187 average time/residue: 0.7535 time to fit residues: 148.4255 Evaluate side-chains 125 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 117 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 387 HIS B 17 GLN B 44 GLN B 88 ASN B 268 ASN G 59 ASN N 1 GLN N 31 ASN R 45 GLN R 99 HIS R 140 GLN R 338 ASN R 407 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.169476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105726 restraints weight = 12029.039| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.97 r_work: 0.3180 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10385 Z= 0.146 Angle : 0.613 8.685 14098 Z= 0.331 Chirality : 0.043 0.138 1542 Planarity : 0.005 0.042 1793 Dihedral : 5.293 50.659 1435 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.74 % Allowed : 10.37 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.23), residues: 1240 helix: 0.74 (0.22), residues: 535 sheet: -0.36 (0.31), residues: 246 loop : -0.30 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 64 TYR 0.035 0.002 TYR R 148 PHE 0.016 0.002 PHE A 212 TRP 0.022 0.002 TRP R 87 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00310 (10379) covalent geometry : angle 0.61117 (14086) SS BOND : bond 0.01093 ( 6) SS BOND : angle 1.89915 ( 12) hydrogen bonds : bond 0.05496 ( 525) hydrogen bonds : angle 5.15586 ( 1485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8425 (mm-30) REVERT: A 347 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8218 (ttm170) REVERT: B 59 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: B 188 MET cc_start: 0.9240 (mmm) cc_final: 0.9026 (mmm) REVERT: B 217 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8704 (pmt) REVERT: G 20 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7893 (mtpt) REVERT: R 45 GLN cc_start: 0.7962 (mt0) cc_final: 0.7728 (mp10) REVERT: R 68 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5670 (pp20) REVERT: R 215 ASP cc_start: 0.7198 (p0) cc_final: 0.6685 (m-30) REVERT: R 380 ARG cc_start: 0.5524 (mmp80) cc_final: 0.5182 (mmm160) REVERT: R 411 LEU cc_start: 0.8341 (tt) cc_final: 0.8085 (tm) outliers start: 19 outliers final: 3 residues processed: 129 average time/residue: 0.8050 time to fit residues: 109.3658 Evaluate side-chains 114 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 268 ASN B 340 ASN G 59 ASN N 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.169186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104827 restraints weight = 12003.323| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.99 r_work: 0.3174 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10385 Z= 0.133 Angle : 0.551 9.753 14098 Z= 0.297 Chirality : 0.042 0.137 1542 Planarity : 0.004 0.048 1793 Dihedral : 4.841 29.509 1433 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.83 % Allowed : 12.02 % Favored : 86.15 % 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: 0.84 (0.24), residues: 1240 helix: 1.61 (0.22), residues: 536 sheet: -0.18 (0.31), residues: 246 loop : -0.16 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.028 0.002 TYR R 148 PHE 0.014 0.001 PHE R 324 TRP 0.017 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00276 (10379) covalent geometry : angle 0.54936 (14086) SS BOND : bond 0.00373 ( 6) SS BOND : angle 1.49224 ( 12) hydrogen bonds : bond 0.04959 ( 525) hydrogen bonds : angle 4.74732 ( 1485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8251 (ttm170) REVERT: B 59 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8639 (m-80) REVERT: B 214 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7643 (mmt180) REVERT: B 217 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8701 (pmt) REVERT: N 19 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8093 (ttt180) REVERT: R 45 GLN cc_start: 0.7959 (mt0) cc_final: 0.7689 (mp10) REVERT: R 68 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5653 (pp20) REVERT: R 215 ASP cc_start: 0.7186 (p0) cc_final: 0.6642 (m-30) REVERT: R 336 LYS cc_start: 0.7714 (mmtp) cc_final: 0.7502 (mmtm) REVERT: R 344 ASP cc_start: 0.6347 (t0) cc_final: 0.6043 (t0) REVERT: R 380 ARG cc_start: 0.5371 (mmp80) cc_final: 0.5045 (mmm160) outliers start: 20 outliers final: 7 residues processed: 126 average time/residue: 0.8396 time to fit residues: 111.2761 Evaluate side-chains 119 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 0.0370 chunk 64 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.166526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101293 restraints weight = 12061.887| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.00 r_work: 0.3122 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10385 Z= 0.193 Angle : 0.613 8.639 14098 Z= 0.328 Chirality : 0.044 0.157 1542 Planarity : 0.005 0.050 1793 Dihedral : 5.194 30.431 1433 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.74 % Allowed : 13.49 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1240 helix: 1.72 (0.22), residues: 531 sheet: -0.07 (0.31), residues: 255 loop : -0.01 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 421 TYR 0.025 0.002 TYR R 148 PHE 0.021 0.002 PHE B 151 TRP 0.022 0.002 TRP A 234 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00428 (10379) covalent geometry : angle 0.61248 (14086) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.23585 ( 12) hydrogen bonds : bond 0.05510 ( 525) hydrogen bonds : angle 4.89339 ( 1485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7675 (ttmm) REVERT: A 347 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8338 (ttm110) REVERT: B 17 GLN cc_start: 0.7921 (tt0) cc_final: 0.7707 (tm-30) REVERT: B 59 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8787 (m-80) REVERT: B 217 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8712 (pmt) REVERT: G 20 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7948 (mtpt) REVERT: G 46 LYS cc_start: 0.8471 (mmpt) cc_final: 0.8246 (mmmm) REVERT: N 19 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8148 (ttt180) REVERT: R 68 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5753 (pp20) REVERT: R 125 GLU cc_start: 0.5940 (pt0) cc_final: 0.5667 (pp20) REVERT: R 215 ASP cc_start: 0.7517 (p0) cc_final: 0.6895 (m-30) REVERT: R 336 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7481 (mmtm) REVERT: R 344 ASP cc_start: 0.6352 (t0) cc_final: 0.6083 (t0) REVERT: R 369 PHE cc_start: 0.5667 (m-10) cc_final: 0.5461 (m-10) REVERT: R 380 ARG cc_start: 0.5366 (mmp80) cc_final: 0.5017 (mmm160) outliers start: 19 outliers final: 6 residues processed: 127 average time/residue: 0.8192 time to fit residues: 109.3912 Evaluate side-chains 122 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 336 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 0.0020 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 16 optimal weight: 0.0030 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 88 ASN B 156 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.169563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105734 restraints weight = 12076.298| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.00 r_work: 0.3191 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 10385 Z= 0.108 Angle : 0.511 8.604 14098 Z= 0.275 Chirality : 0.040 0.139 1542 Planarity : 0.004 0.050 1793 Dihedral : 4.638 25.407 1433 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.47 % Allowed : 14.13 % Favored : 84.40 % 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: 1.32 (0.24), residues: 1240 helix: 2.12 (0.23), residues: 535 sheet: 0.04 (0.31), residues: 259 loop : -0.04 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.025 0.001 TYR R 148 PHE 0.013 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00224 (10379) covalent geometry : angle 0.50912 (14086) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.43629 ( 12) hydrogen bonds : bond 0.04320 ( 525) hydrogen bonds : angle 4.49162 ( 1485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7959 (tt0) cc_final: 0.7710 (tm-30) REVERT: B 59 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8675 (m-80) REVERT: B 214 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7830 (mmt180) REVERT: N 19 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8041 (ttt180) REVERT: N 43 LYS cc_start: 0.8598 (mttt) cc_final: 0.8334 (mtpt) REVERT: R 68 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5604 (pp20) REVERT: R 125 GLU cc_start: 0.5934 (pt0) cc_final: 0.5659 (pp20) REVERT: R 215 ASP cc_start: 0.7451 (p0) cc_final: 0.6810 (m-30) REVERT: R 336 LYS cc_start: 0.7678 (mmtp) cc_final: 0.7378 (mmtm) REVERT: R 344 ASP cc_start: 0.6280 (t0) cc_final: 0.6040 (t0) REVERT: R 369 PHE cc_start: 0.5736 (m-10) cc_final: 0.5469 (m-10) REVERT: R 380 ARG cc_start: 0.5242 (mmp80) cc_final: 0.4904 (mmm160) REVERT: R 411 LEU cc_start: 0.8448 (tt) cc_final: 0.8182 (tm) outliers start: 16 outliers final: 6 residues processed: 123 average time/residue: 0.8303 time to fit residues: 107.4357 Evaluate side-chains 115 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104340 restraints weight = 12106.906| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.00 r_work: 0.3167 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10385 Z= 0.123 Angle : 0.526 8.212 14098 Z= 0.282 Chirality : 0.041 0.141 1542 Planarity : 0.004 0.049 1793 Dihedral : 4.689 26.107 1433 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.56 % Allowed : 14.13 % Favored : 84.31 % 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: 1.45 (0.24), residues: 1240 helix: 2.20 (0.23), residues: 536 sheet: 0.12 (0.32), residues: 249 loop : 0.04 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.024 0.001 TYR R 148 PHE 0.014 0.001 PHE B 151 TRP 0.016 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00263 (10379) covalent geometry : angle 0.52545 (14086) SS BOND : bond 0.00333 ( 6) SS BOND : angle 1.12274 ( 12) hydrogen bonds : bond 0.04489 ( 525) hydrogen bonds : angle 4.49015 ( 1485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8675 (m-80) REVERT: B 214 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7794 (mmt180) REVERT: G 46 LYS cc_start: 0.8466 (mmpt) cc_final: 0.8196 (mmmm) REVERT: N 19 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8019 (ttt180) REVERT: N 43 LYS cc_start: 0.8587 (mttt) cc_final: 0.8337 (mtpt) REVERT: R 68 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.5578 (pp20) REVERT: R 110 TRP cc_start: 0.3929 (m100) cc_final: 0.3366 (m100) REVERT: R 215 ASP cc_start: 0.7500 (p0) cc_final: 0.6871 (m-30) REVERT: R 336 LYS cc_start: 0.7669 (mmtp) cc_final: 0.7357 (mmtm) REVERT: R 344 ASP cc_start: 0.6251 (t0) cc_final: 0.5845 (t0) REVERT: R 380 ARG cc_start: 0.5210 (mmp80) cc_final: 0.4878 (mmm160) REVERT: R 411 LEU cc_start: 0.8456 (tt) cc_final: 0.8188 (tm) outliers start: 17 outliers final: 6 residues processed: 125 average time/residue: 0.8260 time to fit residues: 108.8731 Evaluate side-chains 117 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104271 restraints weight = 11990.978| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.00 r_work: 0.3167 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10385 Z= 0.123 Angle : 0.520 8.092 14098 Z= 0.280 Chirality : 0.041 0.140 1542 Planarity : 0.004 0.050 1793 Dihedral : 4.664 25.372 1433 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.47 % Allowed : 14.31 % Favored : 84.22 % 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: 1.53 (0.24), residues: 1240 helix: 2.24 (0.23), residues: 536 sheet: 0.16 (0.32), residues: 250 loop : 0.12 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.024 0.001 TYR R 148 PHE 0.015 0.001 PHE B 151 TRP 0.016 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00263 (10379) covalent geometry : angle 0.51911 (14086) SS BOND : bond 0.00320 ( 6) SS BOND : angle 1.03970 ( 12) hydrogen bonds : bond 0.04485 ( 525) hydrogen bonds : angle 4.47632 ( 1485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: B 214 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7806 (mmt180) REVERT: G 20 LYS cc_start: 0.8043 (mttp) cc_final: 0.7839 (mttp) REVERT: G 46 LYS cc_start: 0.8486 (mmpt) cc_final: 0.8213 (mmmm) REVERT: N 19 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8014 (ttt180) REVERT: N 43 LYS cc_start: 0.8579 (mttt) cc_final: 0.8328 (mtpt) REVERT: R 68 GLU cc_start: 0.5811 (OUTLIER) cc_final: 0.5541 (pp20) REVERT: R 110 TRP cc_start: 0.3949 (m100) cc_final: 0.3396 (m100) REVERT: R 380 ARG cc_start: 0.5199 (mmp80) cc_final: 0.4873 (mmm160) REVERT: R 411 LEU cc_start: 0.8460 (tt) cc_final: 0.8170 (tm) outliers start: 16 outliers final: 7 residues processed: 117 average time/residue: 0.7750 time to fit residues: 95.6275 Evaluate side-chains 119 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 44 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.168980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104693 restraints weight = 12054.677| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.00 r_work: 0.3169 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10385 Z= 0.118 Angle : 0.526 11.433 14098 Z= 0.280 Chirality : 0.041 0.140 1542 Planarity : 0.004 0.052 1793 Dihedral : 4.636 25.075 1433 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.47 % Allowed : 14.40 % Favored : 84.13 % 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: 1.55 (0.24), residues: 1240 helix: 2.24 (0.23), residues: 536 sheet: 0.21 (0.32), residues: 240 loop : 0.13 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 134 TYR 0.023 0.001 TYR R 148 PHE 0.017 0.001 PHE A 212 TRP 0.016 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00250 (10379) covalent geometry : angle 0.52565 (14086) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.00661 ( 12) hydrogen bonds : bond 0.04376 ( 525) hydrogen bonds : angle 4.43669 ( 1485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: B 9 GLN cc_start: 0.7588 (tp40) cc_final: 0.7332 (tp40) REVERT: B 15 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7769 (mttm) REVERT: B 59 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: B 172 GLU cc_start: 0.8518 (tp30) cc_final: 0.8299 (tp30) REVERT: B 214 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7802 (mmt180) REVERT: G 20 LYS cc_start: 0.8052 (mttp) cc_final: 0.7850 (mttp) REVERT: G 46 LYS cc_start: 0.8492 (mmpt) cc_final: 0.8220 (mmmm) REVERT: N 19 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8009 (ttt180) REVERT: N 43 LYS cc_start: 0.8578 (mttt) cc_final: 0.8339 (mtpt) REVERT: R 68 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5515 (pp20) REVERT: R 110 TRP cc_start: 0.3940 (m100) cc_final: 0.3374 (m100) REVERT: R 114 ASP cc_start: 0.5776 (t0) cc_final: 0.5565 (t70) REVERT: R 336 LYS cc_start: 0.7663 (mmtp) cc_final: 0.7383 (mptt) REVERT: R 380 ARG cc_start: 0.5135 (mmp80) cc_final: 0.4888 (mmp80) REVERT: R 411 LEU cc_start: 0.8471 (tt) cc_final: 0.8190 (tm) outliers start: 16 outliers final: 7 residues processed: 116 average time/residue: 0.8246 time to fit residues: 100.7079 Evaluate side-chains 114 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.0020 chunk 105 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 59 GLN B 16 ASN B 44 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.169575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105444 restraints weight = 12019.693| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.99 r_work: 0.3184 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10385 Z= 0.110 Angle : 0.508 9.758 14098 Z= 0.272 Chirality : 0.041 0.139 1542 Planarity : 0.004 0.049 1793 Dihedral : 4.556 24.310 1433 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.28 % Allowed : 14.68 % Favored : 84.04 % 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 (0.24), residues: 1240 helix: 2.31 (0.23), residues: 536 sheet: 0.22 (0.32), residues: 240 loop : 0.15 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.023 0.001 TYR R 148 PHE 0.016 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00230 (10379) covalent geometry : angle 0.50697 (14086) SS BOND : bond 0.00383 ( 6) SS BOND : angle 1.09707 ( 12) hydrogen bonds : bond 0.04212 ( 525) hydrogen bonds : angle 4.36752 ( 1485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 9 GLN cc_start: 0.7549 (tp40) cc_final: 0.7292 (tp40) REVERT: B 15 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7803 (mttm) REVERT: B 59 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: B 134 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7887 (ptp-110) REVERT: B 214 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7811 (mmt180) REVERT: G 20 LYS cc_start: 0.8075 (mttp) cc_final: 0.7865 (mttp) REVERT: G 46 LYS cc_start: 0.8502 (mmpt) cc_final: 0.8229 (mmmm) REVERT: N 19 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7976 (ttt180) REVERT: N 43 LYS cc_start: 0.8566 (mttt) cc_final: 0.8316 (mtpt) REVERT: R 68 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5507 (pp20) REVERT: R 110 TRP cc_start: 0.3931 (m100) cc_final: 0.3370 (m100) REVERT: R 114 ASP cc_start: 0.5792 (t0) cc_final: 0.5575 (t70) REVERT: R 336 LYS cc_start: 0.7626 (mmtp) cc_final: 0.7346 (mptt) REVERT: R 411 LEU cc_start: 0.8490 (tt) cc_final: 0.8206 (tm) outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.8091 time to fit residues: 100.7637 Evaluate side-chains 115 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 16 ASN B 44 GLN B 88 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.167350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101921 restraints weight = 11961.218| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.06 r_work: 0.3124 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10385 Z= 0.183 Angle : 0.595 9.751 14098 Z= 0.316 Chirality : 0.044 0.147 1542 Planarity : 0.004 0.048 1793 Dihedral : 4.946 25.823 1433 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.19 % Allowed : 15.14 % Favored : 83.67 % 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: 1.54 (0.24), residues: 1240 helix: 2.16 (0.22), residues: 531 sheet: 0.30 (0.33), residues: 242 loop : 0.19 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 197 TYR 0.022 0.002 TYR R 148 PHE 0.021 0.002 PHE B 151 TRP 0.020 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00409 (10379) covalent geometry : angle 0.59379 (14086) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.17883 ( 12) hydrogen bonds : bond 0.05056 ( 525) hydrogen bonds : angle 4.63224 ( 1485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: B 9 GLN cc_start: 0.7633 (tp40) cc_final: 0.7384 (tp40) REVERT: B 59 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: B 134 ARG cc_start: 0.8208 (ptm-80) cc_final: 0.7963 (ptp-110) REVERT: B 214 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7783 (mmt180) REVERT: G 46 LYS cc_start: 0.8551 (mmpt) cc_final: 0.8325 (mmmm) REVERT: N 19 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8063 (ttt180) REVERT: N 43 LYS cc_start: 0.8627 (mttt) cc_final: 0.8381 (mtpt) REVERT: R 68 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5578 (pp20) REVERT: R 110 TRP cc_start: 0.4012 (m100) cc_final: 0.3467 (m100) REVERT: R 114 ASP cc_start: 0.5663 (t0) cc_final: 0.5446 (t0) outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.8460 time to fit residues: 102.5575 Evaluate side-chains 114 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 61 optimal weight: 0.0270 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 44 GLN B 88 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.170111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105789 restraints weight = 12040.728| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.13 r_work: 0.3191 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10385 Z= 0.103 Angle : 0.508 9.772 14098 Z= 0.271 Chirality : 0.040 0.142 1542 Planarity : 0.004 0.049 1793 Dihedral : 4.490 23.830 1433 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.83 % Allowed : 15.41 % Favored : 83.76 % 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: 1240 helix: 2.41 (0.23), residues: 530 sheet: 0.32 (0.32), residues: 249 loop : 0.21 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.024 0.001 TYR R 148 PHE 0.017 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00213 (10379) covalent geometry : angle 0.50700 (14086) SS BOND : bond 0.00310 ( 6) SS BOND : angle 1.13648 ( 12) hydrogen bonds : bond 0.04062 ( 525) hydrogen bonds : angle 4.32798 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7410.89 seconds wall clock time: 126 minutes 5.00 seconds (7565.00 seconds total)