Starting phenix.real_space_refine on Wed Feb 4 16:59:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d1u_46477/02_2026/9d1u_46477.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d1u_46477/02_2026/9d1u_46477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d1u_46477/02_2026/9d1u_46477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d1u_46477/02_2026/9d1u_46477.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d1u_46477/02_2026/9d1u_46477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d1u_46477/02_2026/9d1u_46477.map" } resolution = 3.7 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= 0.025 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 7317 2.51 5 N 2073 2.21 5 O 2253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 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: 11697 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3899 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Chain: "B" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3899 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Chain: "C" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3899 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Time building chain proxies: 2.74, per 1000 atoms: 0.23 Number of scatterers: 11697 At special positions: 0 Unit cell: (85.1, 86.25, 146.05, 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 2253 8.00 N 2073 7.00 C 7317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 153 " distance=2.01 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 319 " distance=2.02 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 291 " distance=2.04 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 153 " distance=2.01 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 319 " distance=2.02 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 291 " distance=2.04 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 153 " distance=2.02 Simple disulfide: pdb=" SG CYS C 295 " - pdb=" SG CYS C 319 " distance=2.02 Simple disulfide: pdb=" SG CYS C 487 " - pdb=" SG CYS C 491 " 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: 1.00 Conformation dependent library (CDL) restraints added in 576.4 milliseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 36 sheets defined 28.7% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 87 through 94 removed outlier: 5.103A pdb=" N GLY A 92 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.555A pdb=" N THR A 342 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 Processing helix chain 'A' and resid 418 through 470 Processing helix chain 'A' and resid 488 through 497 Processing helix chain 'A' and resid 501 through 514 removed outlier: 4.268A pdb=" N TYR A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 87 through 94 removed outlier: 5.103A pdb=" N GLY B 92 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.558A pdb=" N THR B 342 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 Processing helix chain 'B' and resid 418 through 470 Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 501 through 514 removed outlier: 4.268A pdb=" N TYR B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASP B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU B 508 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 87 through 94 removed outlier: 5.103A pdb=" N GLY C 92 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.556A pdb=" N THR C 342 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 Processing helix chain 'C' and resid 418 through 470 Processing helix chain 'C' and resid 488 through 497 Processing helix chain 'C' and resid 501 through 514 removed outlier: 4.268A pdb=" N TYR C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP C 507 " --> pdb=" O ASN C 503 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU C 508 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 379 removed outlier: 3.511A pdb=" N GLY A 374 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.064A pdb=" N ILE A 65 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N CYS A 291 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 67 " --> pdb=" O CYS A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.829A pdb=" N LEU A 73 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.949A pdb=" N ASP A 115 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N TRP A 248 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE A 193 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 270 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.949A pdb=" N ASP A 115 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N TRP A 248 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE A 193 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 144 through 145 Processing sheet with id=AB1, first strand: chain 'A' and resid 150 through 154 Processing sheet with id=AB2, first strand: chain 'A' and resid 178 through 183 Processing sheet with id=AB3, first strand: chain 'A' and resid 300 through 302 removed outlier: 4.295A pdb=" N CYS A 295 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 319 " --> pdb=" O ASN A 403 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN A 403 " --> pdb=" O CYS A 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 374 through 379 removed outlier: 3.510A pdb=" N GLY B 374 " --> pdb=" O ASN B 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AB6, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'B' and resid 57 through 58 Processing sheet with id=AB8, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.063A pdb=" N ILE B 65 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N CYS B 291 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 67 " --> pdb=" O CYS B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 72 through 74 removed outlier: 6.830A pdb=" N LEU B 73 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.948A pdb=" N ASP B 115 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N TRP B 248 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE B 193 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY B 270 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.948A pdb=" N ASP B 115 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N TRP B 248 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE B 193 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AC4, first strand: chain 'B' and resid 150 through 154 Processing sheet with id=AC5, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AC6, first strand: chain 'B' and resid 300 through 302 removed outlier: 4.297A pdb=" N CYS B 295 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 319 " --> pdb=" O ASN B 403 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN B 403 " --> pdb=" O CYS B 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 374 through 379 removed outlier: 3.510A pdb=" N GLY C 374 " --> pdb=" O ASN C 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 38 through 40 Processing sheet with id=AC9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AD2, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.063A pdb=" N ILE C 65 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N CYS C 291 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 67 " --> pdb=" O CYS C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 72 through 74 removed outlier: 6.829A pdb=" N LEU C 73 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.948A pdb=" N ASP C 115 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N TRP C 248 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE C 193 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY C 270 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.948A pdb=" N ASP C 115 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N TRP C 248 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE C 193 " --> pdb=" O PRO C 268 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'C' and resid 150 through 154 Processing sheet with id=AD8, first strand: chain 'C' and resid 178 through 183 Processing sheet with id=AD9, first strand: chain 'C' and resid 300 through 302 removed outlier: 4.295A pdb=" N CYS C 295 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS C 319 " --> pdb=" O ASN C 403 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN C 403 " --> pdb=" O CYS C 319 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2249 1.33 - 1.46: 4264 1.46 - 1.58: 5358 1.58 - 1.70: 0 1.70 - 1.83: 72 Bond restraints: 11943 Sorted by residual: bond pdb=" NE ARG B 335 " pdb=" CZ ARG B 335 " ideal model delta sigma weight residual 1.326 1.241 0.085 1.10e-02 8.26e+03 6.01e+01 bond pdb=" NE ARG C 335 " pdb=" CZ ARG C 335 " ideal model delta sigma weight residual 1.326 1.258 0.068 1.10e-02 8.26e+03 3.84e+01 bond pdb=" CA GLU C 339 " pdb=" C GLU C 339 " ideal model delta sigma weight residual 1.519 1.463 0.056 1.14e-02 7.69e+03 2.45e+01 bond pdb=" CA GLU B 339 " pdb=" C GLU B 339 " ideal model delta sigma weight residual 1.519 1.464 0.055 1.14e-02 7.69e+03 2.34e+01 bond pdb=" CA GLU A 339 " pdb=" C GLU A 339 " ideal model delta sigma weight residual 1.519 1.465 0.054 1.14e-02 7.69e+03 2.27e+01 ... (remaining 11938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 15251 3.68 - 7.35: 881 7.35 - 11.03: 23 11.03 - 14.71: 3 14.71 - 18.39: 3 Bond angle restraints: 16161 Sorted by residual: angle pdb=" CA GLU B 339 " pdb=" CB GLU B 339 " pdb=" CG GLU B 339 " ideal model delta sigma weight residual 114.10 132.49 -18.39 2.00e+00 2.50e-01 8.45e+01 angle pdb=" CA GLU C 339 " pdb=" CB GLU C 339 " pdb=" CG GLU C 339 " ideal model delta sigma weight residual 114.10 131.84 -17.74 2.00e+00 2.50e-01 7.87e+01 angle pdb=" CA GLU A 339 " pdb=" CB GLU A 339 " pdb=" CG GLU A 339 " ideal model delta sigma weight residual 114.10 130.87 -16.77 2.00e+00 2.50e-01 7.03e+01 angle pdb=" N ARG B 419 " pdb=" CA ARG B 419 " pdb=" C ARG B 419 " ideal model delta sigma weight residual 111.07 118.33 -7.26 1.07e+00 8.73e-01 4.60e+01 angle pdb=" N ARG C 419 " pdb=" CA ARG C 419 " pdb=" C ARG C 419 " ideal model delta sigma weight residual 111.07 118.31 -7.24 1.07e+00 8.73e-01 4.58e+01 ... (remaining 16156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 6714 18.00 - 36.00: 378 36.00 - 53.99: 96 53.99 - 71.99: 21 71.99 - 89.99: 24 Dihedral angle restraints: 7233 sinusoidal: 2970 harmonic: 4263 Sorted by residual: dihedral pdb=" CA GLY C 148 " pdb=" C GLY C 148 " pdb=" N THR C 149 " pdb=" CA THR C 149 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLY A 148 " pdb=" C GLY A 148 " pdb=" N THR A 149 " pdb=" CA THR A 149 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLY B 148 " pdb=" C GLY B 148 " pdb=" N THR B 149 " pdb=" CA THR B 149 " ideal model delta harmonic sigma weight residual -180.00 -155.21 -24.79 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 7230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1313 0.104 - 0.207: 351 0.207 - 0.311: 67 0.311 - 0.415: 12 0.415 - 0.519: 6 Chirality restraints: 1749 Sorted by residual: chirality pdb=" CA ASP C 239 " pdb=" N ASP C 239 " pdb=" C ASP C 239 " pdb=" CB ASP C 239 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CA ASP B 239 " pdb=" N ASP B 239 " pdb=" C ASP B 239 " pdb=" CB ASP B 239 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" CA ASP A 239 " pdb=" N ASP A 239 " pdb=" C ASP A 239 " pdb=" CB ASP A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 ... (remaining 1746 not shown) Planarity restraints: 2121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 192 " 0.091 2.00e-02 2.50e+03 5.68e-02 6.44e+01 pdb=" CG TYR C 192 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR C 192 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR C 192 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR C 192 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR C 192 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR C 192 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 192 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " 0.091 2.00e-02 2.50e+03 5.67e-02 6.44e+01 pdb=" CG TYR A 192 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 192 " 0.090 2.00e-02 2.50e+03 5.65e-02 6.39e+01 pdb=" CG TYR B 192 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 192 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR B 192 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR B 192 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR B 192 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR B 192 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 192 " 0.098 2.00e-02 2.50e+03 ... (remaining 2118 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 5056 2.96 - 3.45: 11011 3.45 - 3.93: 21633 3.93 - 4.42: 22940 4.42 - 4.90: 38610 Nonbonded interactions: 99250 Sorted by model distance: nonbonded pdb=" N ILE A 516 " pdb=" O ILE A 516 " model vdw 2.476 2.496 nonbonded pdb=" N ILE C 516 " pdb=" O ILE C 516 " model vdw 2.476 2.496 nonbonded pdb=" N ILE B 516 " pdb=" O ILE B 516 " model vdw 2.477 2.496 nonbonded pdb=" OE1 GLU A 428 " pdb=" OH TYR C 426 " model vdw 2.506 3.040 nonbonded pdb=" OH TYR A 426 " pdb=" OE1 GLU B 428 " model vdw 2.506 3.040 ... (remaining 99245 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.950 Find NCS groups from input model: 0.090 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 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 : 0.015 0.085 11961 Z= 0.904 Angle : 1.884 18.386 16197 Z= 1.296 Chirality : 0.101 0.519 1749 Planarity : 0.013 0.122 2121 Dihedral : 13.728 89.990 4443 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.09 % Allowed : 3.26 % Favored : 94.65 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 5.26 % 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: 0.40 (0.20), residues: 1470 helix: 3.21 (0.23), residues: 351 sheet: -0.25 (0.29), residues: 279 loop : -0.88 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.006 ARG B 335 TYR 0.099 0.020 TYR C 192 PHE 0.044 0.010 PHE A 346 TRP 0.046 0.015 TRP B 435 HIS 0.011 0.002 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.01472 (11943) covalent geometry : angle 1.88425 (16161) SS BOND : bond 0.00908 ( 18) SS BOND : angle 1.72864 ( 36) hydrogen bonds : bond 0.18023 ( 513) hydrogen bonds : angle 7.39159 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 316 time to evaluate : 0.584 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 3 residues processed: 333 average time/residue: 0.1460 time to fit residues: 64.8804 Evaluate side-chains 113 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain C residue 218 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 468 GLN B 32 HIS B 377 GLN B 468 GLN C 32 HIS C 403 ASN C 468 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096775 restraints weight = 20859.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100335 restraints weight = 11748.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102701 restraints weight = 7887.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104294 restraints weight = 5896.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105360 restraints weight = 4756.586| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11961 Z= 0.176 Angle : 0.643 9.093 16197 Z= 0.344 Chirality : 0.047 0.145 1749 Planarity : 0.005 0.036 2121 Dihedral : 4.866 24.574 1608 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.18 % Allowed : 9.46 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.54 (0.20), residues: 1470 helix: 2.59 (0.25), residues: 357 sheet: -0.02 (0.28), residues: 285 loop : -0.49 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 470 TYR 0.015 0.002 TYR A 175 PHE 0.014 0.001 PHE B 188 TRP 0.014 0.002 TRP B 364 HIS 0.007 0.002 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00391 (11943) covalent geometry : angle 0.64136 (16161) SS BOND : bond 0.00709 ( 18) SS BOND : angle 1.16197 ( 36) hydrogen bonds : bond 0.05169 ( 513) hydrogen bonds : angle 5.06635 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 261 SER cc_start: 0.9243 (t) cc_final: 0.8687 (p) REVERT: A 452 ASP cc_start: 0.7612 (m-30) cc_final: 0.7406 (m-30) REVERT: B 261 SER cc_start: 0.9245 (t) cc_final: 0.8844 (p) REVERT: C 182 MET cc_start: 0.8024 (mmm) cc_final: 0.7758 (tpp) REVERT: C 261 SER cc_start: 0.9092 (t) cc_final: 0.8702 (p) outliers start: 41 outliers final: 22 residues processed: 166 average time/residue: 0.0932 time to fit residues: 23.8216 Evaluate side-chains 115 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 504 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 468 GLN C 403 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094294 restraints weight = 20513.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096949 restraints weight = 13468.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098777 restraints weight = 9977.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100052 restraints weight = 7971.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100973 restraints weight = 6725.126| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11961 Z= 0.178 Angle : 0.601 9.145 16197 Z= 0.321 Chirality : 0.045 0.147 1749 Planarity : 0.004 0.035 2121 Dihedral : 4.666 19.130 1607 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.17 % Allowed : 12.40 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.65 (0.21), residues: 1470 helix: 2.67 (0.26), residues: 363 sheet: -0.11 (0.28), residues: 303 loop : -0.37 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 275 TYR 0.014 0.001 TYR B 175 PHE 0.015 0.002 PHE C 481 TRP 0.013 0.001 TRP B 435 HIS 0.016 0.002 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00398 (11943) covalent geometry : angle 0.59193 (16161) SS BOND : bond 0.00714 ( 18) SS BOND : angle 2.31567 ( 36) hydrogen bonds : bond 0.05039 ( 513) hydrogen bonds : angle 4.89392 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.491 Fit side-chains REVERT: A 261 SER cc_start: 0.8813 (t) cc_final: 0.8384 (p) REVERT: A 452 ASP cc_start: 0.7574 (m-30) cc_final: 0.7318 (m-30) REVERT: B 261 SER cc_start: 0.9095 (t) cc_final: 0.8683 (p) REVERT: C 261 SER cc_start: 0.8919 (t) cc_final: 0.8533 (p) outliers start: 28 outliers final: 17 residues processed: 108 average time/residue: 0.0877 time to fit residues: 15.3111 Evaluate side-chains 88 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 105 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 GLN C 32 HIS C 403 ASN C 448 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091992 restraints weight = 20671.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.094691 restraints weight = 13446.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096500 restraints weight = 9899.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097783 restraints weight = 7911.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.098673 restraints weight = 6667.396| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11961 Z= 0.156 Angle : 0.587 10.711 16197 Z= 0.306 Chirality : 0.045 0.168 1749 Planarity : 0.004 0.033 2121 Dihedral : 4.564 26.036 1605 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.87 % Allowed : 12.02 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.61 (0.21), residues: 1470 helix: 2.61 (0.26), residues: 363 sheet: -0.08 (0.28), residues: 303 loop : -0.42 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 155 TYR 0.014 0.001 TYR B 175 PHE 0.014 0.002 PHE C 481 TRP 0.010 0.001 TRP A 435 HIS 0.007 0.001 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00357 (11943) covalent geometry : angle 0.57944 (16161) SS BOND : bond 0.00404 ( 18) SS BOND : angle 2.04726 ( 36) hydrogen bonds : bond 0.04788 ( 513) hydrogen bonds : angle 4.85024 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 458 MET cc_start: 0.8335 (tpp) cc_final: 0.7889 (tpp) REVERT: B 261 SER cc_start: 0.9201 (t) cc_final: 0.8698 (p) REVERT: C 261 SER cc_start: 0.9088 (t) cc_final: 0.8701 (p) outliers start: 37 outliers final: 18 residues processed: 103 average time/residue: 0.0926 time to fit residues: 15.0173 Evaluate side-chains 77 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 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 230 ASN A 448 GLN C 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.089201 restraints weight = 20807.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091823 restraints weight = 13694.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093602 restraints weight = 10132.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094857 restraints weight = 8131.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095743 restraints weight = 6869.272| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11961 Z= 0.175 Angle : 0.606 10.782 16197 Z= 0.315 Chirality : 0.045 0.151 1749 Planarity : 0.004 0.035 2121 Dihedral : 4.578 24.585 1605 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.40 % Allowed : 12.87 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.60 (0.21), residues: 1470 helix: 2.66 (0.26), residues: 357 sheet: -0.04 (0.29), residues: 303 loop : -0.44 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 155 TYR 0.013 0.001 TYR B 365 PHE 0.020 0.002 PHE B 481 TRP 0.009 0.001 TRP A 435 HIS 0.011 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00405 (11943) covalent geometry : angle 0.59386 (16161) SS BOND : bond 0.00745 ( 18) SS BOND : angle 2.64395 ( 36) hydrogen bonds : bond 0.04849 ( 513) hydrogen bonds : angle 4.82544 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.468 Fit side-chains REVERT: B 458 MET cc_start: 0.8274 (tpp) cc_final: 0.7551 (tpp) outliers start: 31 outliers final: 26 residues processed: 88 average time/residue: 0.0924 time to fit residues: 12.9445 Evaluate side-chains 76 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 495 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 55 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.089004 restraints weight = 20775.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091630 restraints weight = 13485.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.093487 restraints weight = 9916.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094781 restraints weight = 7875.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095722 restraints weight = 6622.826| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.7729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11961 Z= 0.150 Angle : 0.566 12.178 16197 Z= 0.292 Chirality : 0.044 0.146 1749 Planarity : 0.003 0.036 2121 Dihedral : 4.406 25.789 1605 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.25 % Allowed : 13.64 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.69 (0.21), residues: 1470 helix: 2.84 (0.26), residues: 357 sheet: -0.08 (0.29), residues: 303 loop : -0.40 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 47 TYR 0.010 0.001 TYR B 505 PHE 0.018 0.002 PHE B 481 TRP 0.011 0.001 TRP B 435 HIS 0.010 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00347 (11943) covalent geometry : angle 0.55803 (16161) SS BOND : bond 0.00612 ( 18) SS BOND : angle 2.11197 ( 36) hydrogen bonds : bond 0.04611 ( 513) hydrogen bonds : angle 4.69711 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8729 (tp) cc_final: 0.8523 (tp) outliers start: 29 outliers final: 21 residues processed: 76 average time/residue: 0.0979 time to fit residues: 11.7769 Evaluate side-chains 70 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 81 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 0.0010 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090211 restraints weight = 20607.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092883 restraints weight = 13409.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094754 restraints weight = 9892.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096118 restraints weight = 7876.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097031 restraints weight = 6601.835| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.7925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11961 Z= 0.128 Angle : 0.547 12.882 16197 Z= 0.283 Chirality : 0.043 0.142 1749 Planarity : 0.003 0.038 2121 Dihedral : 4.244 25.118 1605 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.02 % Allowed : 13.80 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.78 (0.22), residues: 1470 helix: 3.05 (0.26), residues: 357 sheet: -0.06 (0.29), residues: 303 loop : -0.40 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 275 TYR 0.013 0.001 TYR B 365 PHE 0.016 0.001 PHE B 481 TRP 0.010 0.001 TRP A 435 HIS 0.011 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00295 (11943) covalent geometry : angle 0.53920 (16161) SS BOND : bond 0.00405 ( 18) SS BOND : angle 2.03647 ( 36) hydrogen bonds : bond 0.04407 ( 513) hydrogen bonds : angle 4.59526 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: B 458 MET cc_start: 0.8440 (tpp) cc_final: 0.7839 (tpp) outliers start: 26 outliers final: 23 residues processed: 71 average time/residue: 0.0988 time to fit residues: 11.0846 Evaluate side-chains 72 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 453 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081665 restraints weight = 21389.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.084544 restraints weight = 13328.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.086564 restraints weight = 9577.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088011 restraints weight = 7533.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088964 restraints weight = 6277.180| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.8089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 11961 Z= 0.138 Angle : 0.552 12.845 16197 Z= 0.287 Chirality : 0.043 0.142 1749 Planarity : 0.003 0.039 2121 Dihedral : 4.206 24.956 1605 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.09 % Allowed : 13.72 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.80 (0.22), residues: 1470 helix: 3.10 (0.26), residues: 357 sheet: -0.14 (0.29), residues: 318 loop : -0.36 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 275 TYR 0.012 0.001 TYR A 365 PHE 0.015 0.001 PHE B 481 TRP 0.009 0.001 TRP A 435 HIS 0.010 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00325 (11943) covalent geometry : angle 0.54462 (16161) SS BOND : bond 0.00424 ( 18) SS BOND : angle 1.92528 ( 36) hydrogen bonds : bond 0.04400 ( 513) hydrogen bonds : angle 4.58582 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.432 Fit side-chains REVERT: C 240 ILE cc_start: 0.9162 (mm) cc_final: 0.8942 (mp) outliers start: 27 outliers final: 19 residues processed: 71 average time/residue: 0.1000 time to fit residues: 11.2344 Evaluate side-chains 68 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 453 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088557 restraints weight = 20752.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091103 restraints weight = 13837.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.092934 restraints weight = 10404.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094190 restraints weight = 8404.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095044 restraints weight = 7158.180| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.8216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11961 Z= 0.200 Angle : 0.604 13.517 16197 Z= 0.314 Chirality : 0.045 0.153 1749 Planarity : 0.004 0.044 2121 Dihedral : 4.430 25.258 1605 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.17 % Allowed : 13.64 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.51 (0.22), residues: 1470 helix: 2.45 (0.26), residues: 375 sheet: -0.33 (0.28), residues: 318 loop : -0.38 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 234 TYR 0.019 0.002 TYR B 365 PHE 0.020 0.002 PHE A 162 TRP 0.011 0.001 TRP A 98 HIS 0.010 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00473 (11943) covalent geometry : angle 0.59652 (16161) SS BOND : bond 0.00512 ( 18) SS BOND : angle 2.05307 ( 36) hydrogen bonds : bond 0.04850 ( 513) hydrogen bonds : angle 4.77635 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: B 458 MET cc_start: 0.8572 (tpp) cc_final: 0.8012 (tpp) outliers start: 28 outliers final: 25 residues processed: 71 average time/residue: 0.0993 time to fit residues: 10.9840 Evaluate side-chains 72 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 495 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.090154 restraints weight = 20820.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092674 restraints weight = 13876.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094508 restraints weight = 10434.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095794 restraints weight = 8411.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096596 restraints weight = 7132.632| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.8278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11961 Z= 0.146 Angle : 0.563 13.903 16197 Z= 0.292 Chirality : 0.044 0.149 1749 Planarity : 0.003 0.044 2121 Dihedral : 4.305 25.481 1605 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.94 % Allowed : 13.88 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.60 (0.22), residues: 1470 helix: 2.99 (0.26), residues: 357 sheet: -0.41 (0.28), residues: 318 loop : -0.45 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 47 TYR 0.013 0.001 TYR B 365 PHE 0.019 0.001 PHE A 162 TRP 0.009 0.001 TRP C 435 HIS 0.010 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00343 (11943) covalent geometry : angle 0.55650 (16161) SS BOND : bond 0.00440 ( 18) SS BOND : angle 1.95123 ( 36) hydrogen bonds : bond 0.04550 ( 513) hydrogen bonds : angle 4.64787 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: B 458 MET cc_start: 0.8508 (tpp) cc_final: 0.7862 (tpp) REVERT: C 47 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7175 (tmm160) REVERT: C 360 MET cc_start: 0.7204 (ttp) cc_final: 0.6986 (ptm) outliers start: 25 outliers final: 24 residues processed: 66 average time/residue: 0.1020 time to fit residues: 10.5440 Evaluate side-chains 71 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090258 restraints weight = 20741.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092758 restraints weight = 13843.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094535 restraints weight = 10407.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095818 restraints weight = 8440.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096734 restraints weight = 7178.365| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.8282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 11961 Z= 0.195 Angle : 0.824 59.199 16197 Z= 0.485 Chirality : 0.050 1.030 1749 Planarity : 0.004 0.134 2121 Dihedral : 4.319 25.378 1605 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.94 % Allowed : 13.80 % Favored : 84.26 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.26 % 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: 0.62 (0.22), residues: 1470 helix: 3.01 (0.26), residues: 357 sheet: -0.40 (0.28), residues: 318 loop : -0.44 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 47 TYR 0.011 0.001 TYR B 365 PHE 0.026 0.002 PHE A 139 TRP 0.009 0.001 TRP C 435 HIS 0.009 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00412 (11943) covalent geometry : angle 0.82027 (16161) SS BOND : bond 0.00431 ( 18) SS BOND : angle 1.93027 ( 36) hydrogen bonds : bond 0.04538 ( 513) hydrogen bonds : angle 4.64818 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.81 seconds wall clock time: 31 minutes 8.56 seconds (1868.56 seconds total)