Starting phenix.real_space_refine on Tue Feb 3 23:45:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jic_61501/02_2026/9jic_61501.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jic_61501/02_2026/9jic_61501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jic_61501/02_2026/9jic_61501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jic_61501/02_2026/9jic_61501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jic_61501/02_2026/9jic_61501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jic_61501/02_2026/9jic_61501.map" } resolution = 3.4 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= -0.002 sd= 0.033 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 54 5.16 5 C 4864 2.51 5 N 1331 2.21 5 O 1433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7682 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1892 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain breaks: 3 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 4, 'PHE:plan': 11, 'ASN:plan1': 3, 'TYR:plan': 3, 'ASP:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 190 Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1674 Classifications: {'peptide': 213} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 210} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2483 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 227 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 32} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "S" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1406 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 5 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 83 Time building chain proxies: 1.85, per 1000 atoms: 0.24 Number of scatterers: 7682 At special positions: 0 Unit cell: (87.55, 117.3, 129.2, 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 54 16.00 O 1433 8.00 N 1331 7.00 C 4864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 0.73 Conformation dependent library (CDL) restraints added in 310.4 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 13 sheets defined 36.6% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 29 through 55 removed outlier: 3.580A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.699A pdb=" N LEU A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 97 through 130 removed outlier: 4.018A pdb=" N LEU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 164 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 188 through 217 removed outlier: 4.160A pdb=" N MET A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 224 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 298 removed outlier: 4.052A pdb=" N SER A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.765A pdb=" N TYR A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 4.123A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.099A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 removed outlier: 3.522A pdb=" N GLU C 216 " --> pdb=" O HIS C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 213 through 216' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.515A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.637A pdb=" N ASP C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.217A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.737A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.636A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 190 removed outlier: 4.095A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.791A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.793A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.739A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.781A 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: 3.618A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.067A 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: 3.548A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.948A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.550A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.544A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.326A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.326A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.847A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.720A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1152 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: 1.13 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1440 1.32 - 1.45: 2136 1.45 - 1.57: 4198 1.57 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 7846 Sorted by residual: bond pdb=" CA LEU A 280 " pdb=" C LEU A 280 " ideal model delta sigma weight residual 1.522 1.467 0.056 1.36e-02 5.41e+03 1.67e+01 bond pdb=" N ASP A 85 " pdb=" CA ASP A 85 " ideal model delta sigma weight residual 1.458 1.404 0.054 1.33e-02 5.65e+03 1.63e+01 bond pdb=" CA MET A 84 " pdb=" C MET A 84 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" CA ASP A 85 " pdb=" C ASP A 85 " ideal model delta sigma weight residual 1.522 1.469 0.054 1.40e-02 5.10e+03 1.48e+01 bond pdb=" C TYR A 86 " pdb=" N TYR A 87 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.30e-02 5.92e+03 1.45e+01 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 10386 2.22 - 4.45: 244 4.45 - 6.67: 39 6.67 - 8.89: 6 8.89 - 11.12: 1 Bond angle restraints: 10676 Sorted by residual: angle pdb=" C LYS A 57 " pdb=" CA LYS A 57 " pdb=" CB LYS A 57 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.55e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.53 109.80 3.73 9.80e-01 1.04e+00 1.45e+01 angle pdb=" N MET C 243 " pdb=" CA MET C 243 " pdb=" C MET C 243 " ideal model delta sigma weight residual 111.07 107.03 4.04 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N LEU C 23 " pdb=" CA LEU C 23 " pdb=" C LEU C 23 " ideal model delta sigma weight residual 110.97 106.92 4.05 1.09e+00 8.42e-01 1.38e+01 angle pdb=" N THR A 159 " pdb=" CA THR A 159 " pdb=" C THR A 159 " ideal model delta sigma weight residual 111.07 107.12 3.95 1.07e+00 8.73e-01 1.36e+01 ... (remaining 10671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4077 17.74 - 35.49: 398 35.49 - 53.23: 79 53.23 - 70.98: 6 70.98 - 88.72: 7 Dihedral angle restraints: 4567 sinusoidal: 1516 harmonic: 3051 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual 93.00 -178.28 -88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 147.12 -54.12 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual -86.00 -124.05 38.05 1 1.00e+01 1.00e-02 2.04e+01 ... (remaining 4564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1005 0.057 - 0.114: 186 0.114 - 0.171: 27 0.171 - 0.227: 3 0.227 - 0.284: 1 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CG LEU A 163 " pdb=" CB LEU A 163 " pdb=" CD1 LEU A 163 " pdb=" CD2 LEU A 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CG LEU C 268 " pdb=" CB LEU C 268 " pdb=" CD1 LEU C 268 " pdb=" CD2 LEU C 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ARG A 89 " pdb=" N ARG A 89 " pdb=" C ARG A 89 " pdb=" CB ARG A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 1219 not shown) Planarity restraints: 1369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 69 " 0.015 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU A 69 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU A 69 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA A 70 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 290 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO A 291 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 31 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO A 32 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.038 5.00e-02 4.00e+02 ... (remaining 1366 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 2 1.90 - 2.65: 185 2.65 - 3.40: 11073 3.40 - 4.15: 17741 4.15 - 4.90: 31747 Nonbonded interactions: 60748 Sorted by model distance: nonbonded pdb=" O VAL A 160 " pdb=" CD2 LEU A 163 " model vdw 1.151 3.460 nonbonded pdb=" O THR A 159 " pdb=" CD1 LEU A 163 " model vdw 1.388 3.460 nonbonded pdb=" C VAL A 160 " pdb=" CD2 LEU A 163 " model vdw 1.984 3.690 nonbonded pdb=" C THR A 159 " pdb=" CD1 LEU A 163 " model vdw 2.031 3.690 nonbonded pdb=" CA VAL A 160 " pdb=" CD1 LEU A 163 " model vdw 2.211 3.890 ... (remaining 60743 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: 2.080 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.660 Find NCS groups from input model: 0.030 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7851 Z= 0.372 Angle : 0.769 11.116 10686 Z= 0.458 Chirality : 0.045 0.284 1222 Planarity : 0.005 0.077 1369 Dihedral : 14.448 88.117 2574 Min Nonbonded Distance : 1.151 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.25 % Favored : 93.46 % Rotamer: Outliers : 0.55 % Allowed : 20.08 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.27), residues: 1024 helix: 0.83 (0.30), residues: 349 sheet: 0.16 (0.33), residues: 243 loop : -1.34 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 208 TYR 0.018 0.001 TYR C 290 PHE 0.011 0.001 PHE A 117 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 7846) covalent geometry : angle 0.76888 (10676) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.77922 ( 10) hydrogen bonds : bond 0.21200 ( 393) hydrogen bonds : angle 7.57419 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.7772 (ppp) cc_final: 0.7478 (ppp) REVERT: S 166 LEU cc_start: 0.9229 (tp) cc_final: 0.8616 (tt) REVERT: S 176 LEU cc_start: 0.9677 (mt) cc_final: 0.9460 (mt) REVERT: S 200 PHE cc_start: 0.8992 (m-80) cc_final: 0.8725 (m-80) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.1254 time to fit residues: 14.5144 Evaluate side-chains 70 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 183 HIS B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.081266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051684 restraints weight = 31495.029| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 5.15 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7851 Z= 0.283 Angle : 0.693 16.536 10686 Z= 0.361 Chirality : 0.045 0.366 1222 Planarity : 0.005 0.069 1369 Dihedral : 4.734 59.379 1118 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 3.44 % Allowed : 20.77 % Favored : 75.79 % 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: -0.00 (0.27), residues: 1024 helix: 1.62 (0.29), residues: 353 sheet: -0.06 (0.33), residues: 253 loop : -1.39 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 111 TYR 0.019 0.002 TYR S 60 PHE 0.014 0.001 PHE C 223 TRP 0.024 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 7846) covalent geometry : angle 0.69238 (10676) SS BOND : bond 0.00331 ( 5) SS BOND : angle 1.12117 ( 10) hydrogen bonds : bond 0.05134 ( 393) hydrogen bonds : angle 5.30453 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8428 (p0) REVERT: C 6 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8231 (p) REVERT: S 128 MET cc_start: 0.6352 (tpp) cc_final: 0.5936 (tpp) REVERT: S 174 GLN cc_start: 0.8669 (pm20) cc_final: 0.8215 (pm20) outliers start: 25 outliers final: 16 residues processed: 94 average time/residue: 0.0820 time to fit residues: 10.9291 Evaluate side-chains 83 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.082099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052730 restraints weight = 30995.968| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 5.09 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7851 Z= 0.170 Angle : 0.615 17.059 10686 Z= 0.312 Chirality : 0.042 0.210 1222 Planarity : 0.004 0.068 1369 Dihedral : 4.432 52.751 1118 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 3.71 % Allowed : 21.73 % Favored : 74.55 % 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: 0.34 (0.27), residues: 1024 helix: 2.05 (0.29), residues: 355 sheet: 0.00 (0.32), residues: 256 loop : -1.28 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 208 TYR 0.016 0.001 TYR S 178 PHE 0.015 0.001 PHE A 105 TRP 0.014 0.001 TRP A 93 HIS 0.002 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7846) covalent geometry : angle 0.61494 (10676) SS BOND : bond 0.00291 ( 5) SS BOND : angle 0.82169 ( 10) hydrogen bonds : bond 0.04268 ( 393) hydrogen bonds : angle 4.72345 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8738 (mmm-85) REVERT: C 6 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8164 (p) REVERT: B 188 MET cc_start: 0.9203 (mmp) cc_final: 0.8784 (mmp) REVERT: B 262 MET cc_start: 0.7983 (ppp) cc_final: 0.7626 (ppp) REVERT: S 128 MET cc_start: 0.6961 (tpp) cc_final: 0.6298 (tpp) outliers start: 27 outliers final: 17 residues processed: 94 average time/residue: 0.0952 time to fit residues: 12.1722 Evaluate side-chains 84 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.082614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053300 restraints weight = 31830.154| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 5.17 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7851 Z= 0.132 Angle : 0.596 16.573 10686 Z= 0.301 Chirality : 0.042 0.211 1222 Planarity : 0.004 0.067 1369 Dihedral : 4.234 51.326 1118 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 3.44 % Allowed : 21.32 % Favored : 75.24 % 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: 0.34 (0.28), residues: 1024 helix: 1.95 (0.29), residues: 367 sheet: -0.09 (0.31), residues: 258 loop : -1.20 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 111 TYR 0.013 0.001 TYR S 178 PHE 0.009 0.001 PHE C 189 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7846) covalent geometry : angle 0.59578 (10676) SS BOND : bond 0.00310 ( 5) SS BOND : angle 0.73280 ( 10) hydrogen bonds : bond 0.03755 ( 393) hydrogen bonds : angle 4.47239 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8728 (mmm-85) REVERT: B 188 MET cc_start: 0.9207 (mmp) cc_final: 0.8969 (mmp) REVERT: B 217 MET cc_start: 0.9323 (ppp) cc_final: 0.9037 (ppp) REVERT: B 262 MET cc_start: 0.7962 (ppp) cc_final: 0.7612 (ppp) REVERT: S 128 MET cc_start: 0.7392 (tpp) cc_final: 0.7160 (tpp) outliers start: 25 outliers final: 21 residues processed: 93 average time/residue: 0.0769 time to fit residues: 9.9260 Evaluate side-chains 90 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 56 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 50.0000 chunk 98 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 295 ASN ** 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 = 0.3892 r_free = 0.3892 target = 0.086079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057097 restraints weight = 30373.004| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 5.22 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7851 Z= 0.151 Angle : 0.599 16.099 10686 Z= 0.303 Chirality : 0.042 0.207 1222 Planarity : 0.004 0.066 1369 Dihedral : 4.187 49.445 1118 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 3.99 % Allowed : 20.50 % Favored : 75.52 % 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: 0.43 (0.28), residues: 1024 helix: 2.04 (0.29), residues: 367 sheet: -0.09 (0.31), residues: 260 loop : -1.13 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 208 TYR 0.011 0.001 TYR S 178 PHE 0.016 0.001 PHE A 105 TRP 0.011 0.001 TRP A 50 HIS 0.002 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7846) covalent geometry : angle 0.59901 (10676) SS BOND : bond 0.00352 ( 5) SS BOND : angle 0.79731 ( 10) hydrogen bonds : bond 0.03694 ( 393) hydrogen bonds : angle 4.36681 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8725 (mmm-85) REVERT: C 6 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.8029 (p) REVERT: C 305 CYS cc_start: 0.9517 (m) cc_final: 0.9253 (m) REVERT: B 176 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8989 (mm-40) REVERT: B 188 MET cc_start: 0.9255 (mmp) cc_final: 0.8971 (mmp) REVERT: B 262 MET cc_start: 0.7935 (ppp) cc_final: 0.7564 (ppp) REVERT: S 128 MET cc_start: 0.7481 (tpp) cc_final: 0.7151 (tpp) REVERT: S 198 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8637 (m) outliers start: 29 outliers final: 24 residues processed: 97 average time/residue: 0.0966 time to fit residues: 12.4614 Evaluate side-chains 94 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 85 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 295 ASN ** 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 = 0.3779 r_free = 0.3779 target = 0.083433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053746 restraints weight = 31006.842| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 5.20 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7851 Z= 0.122 Angle : 0.601 16.096 10686 Z= 0.300 Chirality : 0.042 0.199 1222 Planarity : 0.004 0.082 1369 Dihedral : 4.181 53.651 1118 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 3.58 % Allowed : 21.46 % Favored : 74.97 % 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: 0.43 (0.27), residues: 1024 helix: 2.03 (0.28), residues: 368 sheet: 0.01 (0.32), residues: 239 loop : -1.16 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 111 TYR 0.014 0.001 TYR C 290 PHE 0.009 0.001 PHE C 189 TRP 0.013 0.001 TRP A 50 HIS 0.002 0.000 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7846) covalent geometry : angle 0.60099 (10676) SS BOND : bond 0.00335 ( 5) SS BOND : angle 0.62832 ( 10) hydrogen bonds : bond 0.03470 ( 393) hydrogen bonds : angle 4.28084 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8963 (mmm-85) cc_final: 0.8728 (mmm-85) REVERT: C 6 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7885 (p) REVERT: C 290 TYR cc_start: 0.8519 (t80) cc_final: 0.8244 (t80) REVERT: C 305 CYS cc_start: 0.9552 (m) cc_final: 0.9285 (m) REVERT: C 308 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8594 (pm20) REVERT: B 176 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8964 (mm-40) REVERT: B 188 MET cc_start: 0.9218 (mmp) cc_final: 0.8897 (mmp) REVERT: B 262 MET cc_start: 0.7932 (ppp) cc_final: 0.7552 (ppp) REVERT: S 128 MET cc_start: 0.7660 (tpp) cc_final: 0.7261 (tpp) outliers start: 26 outliers final: 20 residues processed: 93 average time/residue: 0.0869 time to fit residues: 11.1131 Evaluate side-chains 91 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 14 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 61 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 295 ASN ** 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 = 0.3768 r_free = 0.3768 target = 0.082766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052898 restraints weight = 30710.501| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 5.18 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7851 Z= 0.172 Angle : 0.616 15.562 10686 Z= 0.313 Chirality : 0.042 0.200 1222 Planarity : 0.004 0.077 1369 Dihedral : 4.193 49.819 1118 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 4.40 % Allowed : 21.05 % Favored : 74.55 % 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: 0.44 (0.28), residues: 1024 helix: 2.07 (0.29), residues: 371 sheet: 0.01 (0.32), residues: 250 loop : -1.23 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 148 TYR 0.012 0.001 TYR S 60 PHE 0.009 0.001 PHE C 223 TRP 0.014 0.001 TRP A 50 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7846) covalent geometry : angle 0.61619 (10676) SS BOND : bond 0.00321 ( 5) SS BOND : angle 0.73605 ( 10) hydrogen bonds : bond 0.03611 ( 393) hydrogen bonds : angle 4.29863 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8968 (mmm-85) cc_final: 0.8732 (mmm-85) REVERT: C 6 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7951 (p) REVERT: C 290 TYR cc_start: 0.8573 (t80) cc_final: 0.8285 (t80) REVERT: C 305 CYS cc_start: 0.9568 (m) cc_final: 0.9311 (m) REVERT: C 308 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: B 45 MET cc_start: 0.8914 (mtt) cc_final: 0.8687 (mtt) REVERT: B 176 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8956 (mm-40) REVERT: B 188 MET cc_start: 0.9206 (mmp) cc_final: 0.8872 (mmp) REVERT: B 262 MET cc_start: 0.8002 (ppp) cc_final: 0.7630 (ppp) REVERT: B 301 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8566 (mmmt) REVERT: S 128 MET cc_start: 0.7689 (tpp) cc_final: 0.7261 (tpp) outliers start: 32 outliers final: 26 residues processed: 94 average time/residue: 0.0842 time to fit residues: 11.0832 Evaluate side-chains 95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.083909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054518 restraints weight = 30808.213| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 5.12 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7851 Z= 0.110 Angle : 0.605 15.891 10686 Z= 0.301 Chirality : 0.042 0.192 1222 Planarity : 0.004 0.063 1369 Dihedral : 4.108 54.727 1118 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.31 % Rotamer: Outliers : 3.44 % Allowed : 21.60 % Favored : 74.97 % 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: 0.43 (0.27), residues: 1024 helix: 1.98 (0.28), residues: 373 sheet: 0.05 (0.32), residues: 241 loop : -1.18 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 111 TYR 0.010 0.001 TYR C 290 PHE 0.021 0.001 PHE A 105 TRP 0.013 0.001 TRP A 50 HIS 0.002 0.000 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7846) covalent geometry : angle 0.60521 (10676) SS BOND : bond 0.00322 ( 5) SS BOND : angle 0.63188 ( 10) hydrogen bonds : bond 0.03250 ( 393) hydrogen bonds : angle 4.16935 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8727 (mmm-85) REVERT: C 290 TYR cc_start: 0.8548 (t80) cc_final: 0.8271 (t80) REVERT: C 305 CYS cc_start: 0.9556 (m) cc_final: 0.9262 (m) REVERT: C 306 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8599 (mp10) REVERT: C 308 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8596 (pm20) REVERT: B 176 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9011 (mm-40) REVERT: B 188 MET cc_start: 0.9277 (mmp) cc_final: 0.8926 (mmp) REVERT: B 262 MET cc_start: 0.8125 (ppp) cc_final: 0.7711 (ppp) REVERT: B 301 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8628 (mmmt) outliers start: 25 outliers final: 21 residues processed: 98 average time/residue: 0.1034 time to fit residues: 13.6031 Evaluate side-chains 93 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 97 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 50.0000 chunk 92 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 13 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.084181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054766 restraints weight = 30542.348| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 5.16 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7851 Z= 0.110 Angle : 0.620 15.614 10686 Z= 0.306 Chirality : 0.042 0.184 1222 Planarity : 0.004 0.075 1369 Dihedral : 4.041 56.670 1118 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.59 % Favored : 95.21 % Rotamer: Outliers : 3.30 % Allowed : 22.15 % Favored : 74.55 % 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: 0.50 (0.27), residues: 1024 helix: 2.01 (0.28), residues: 371 sheet: 0.27 (0.33), residues: 234 loop : -1.19 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 111 TYR 0.010 0.001 TYR S 178 PHE 0.018 0.001 PHE A 105 TRP 0.012 0.001 TRP A 50 HIS 0.003 0.000 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7846) covalent geometry : angle 0.61898 (10676) SS BOND : bond 0.00406 ( 5) SS BOND : angle 1.04621 ( 10) hydrogen bonds : bond 0.03190 ( 393) hydrogen bonds : angle 4.15839 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8557 (tpt-90) REVERT: C 6 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7762 (p) REVERT: C 243 MET cc_start: 0.9045 (mmt) cc_final: 0.8835 (mmt) REVERT: C 290 TYR cc_start: 0.8641 (t80) cc_final: 0.8340 (t80) REVERT: C 305 CYS cc_start: 0.9565 (m) cc_final: 0.9314 (m) REVERT: C 307 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8614 (t80) REVERT: C 308 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: B 262 MET cc_start: 0.8063 (ppp) cc_final: 0.7671 (ppp) REVERT: S 128 MET cc_start: 0.7499 (tpp) cc_final: 0.6487 (tpp) REVERT: S 223 TYR cc_start: 0.6933 (m-80) cc_final: 0.6412 (m-80) outliers start: 24 outliers final: 19 residues processed: 96 average time/residue: 0.0733 time to fit residues: 9.6994 Evaluate side-chains 94 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.084215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054936 restraints weight = 30647.202| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 5.11 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7851 Z= 0.109 Angle : 0.629 15.454 10686 Z= 0.310 Chirality : 0.042 0.177 1222 Planarity : 0.004 0.062 1369 Dihedral : 4.028 58.552 1118 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 3.16 % Allowed : 22.28 % Favored : 74.55 % 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: 0.52 (0.27), residues: 1024 helix: 2.02 (0.28), residues: 371 sheet: 0.30 (0.33), residues: 234 loop : -1.19 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 111 TYR 0.009 0.001 TYR S 178 PHE 0.020 0.001 PHE A 105 TRP 0.012 0.001 TRP A 50 HIS 0.003 0.000 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7846) covalent geometry : angle 0.62879 (10676) SS BOND : bond 0.00388 ( 5) SS BOND : angle 1.12650 ( 10) hydrogen bonds : bond 0.03098 ( 393) hydrogen bonds : angle 4.12797 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8553 (tpt-90) REVERT: C 6 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7791 (p) REVERT: C 243 MET cc_start: 0.9055 (mmt) cc_final: 0.8805 (mmt) REVERT: C 290 TYR cc_start: 0.8606 (t80) cc_final: 0.8307 (t80) REVERT: C 305 CYS cc_start: 0.9552 (m) cc_final: 0.9294 (m) REVERT: C 307 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8680 (t80) REVERT: C 308 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: B 176 GLN cc_start: 0.9266 (mm-40) cc_final: 0.9018 (mm-40) REVERT: B 188 MET cc_start: 0.9140 (mmp) cc_final: 0.8570 (mmp) REVERT: B 262 MET cc_start: 0.8093 (ppp) cc_final: 0.7679 (ppp) REVERT: S 128 MET cc_start: 0.7557 (tpp) cc_final: 0.6515 (tpp) REVERT: S 223 TYR cc_start: 0.6901 (m-80) cc_final: 0.6394 (m-80) outliers start: 23 outliers final: 18 residues processed: 94 average time/residue: 0.0820 time to fit residues: 10.7360 Evaluate side-chains 94 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 0.4980 chunk 44 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 0.0770 chunk 48 optimal weight: 0.2980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.084773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055562 restraints weight = 30477.847| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 5.17 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7851 Z= 0.104 Angle : 0.618 14.993 10686 Z= 0.304 Chirality : 0.041 0.157 1222 Planarity : 0.004 0.062 1369 Dihedral : 3.890 55.742 1118 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 2.61 % Allowed : 22.56 % Favored : 74.83 % 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: 0.58 (0.27), residues: 1024 helix: 2.14 (0.29), residues: 361 sheet: 0.34 (0.33), residues: 234 loop : -1.15 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 111 TYR 0.009 0.001 TYR S 178 PHE 0.020 0.001 PHE A 105 TRP 0.010 0.001 TRP A 50 HIS 0.003 0.000 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7846) covalent geometry : angle 0.61805 (10676) SS BOND : bond 0.00355 ( 5) SS BOND : angle 0.86539 ( 10) hydrogen bonds : bond 0.02964 ( 393) hydrogen bonds : angle 4.08131 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.23 seconds wall clock time: 28 minutes 5.40 seconds (1685.40 seconds total)