Starting phenix.real_space_refine on Tue Jul 29 12:39:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xuj_33471/07_2025/7xuj_33471.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xuj_33471/07_2025/7xuj_33471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_2025/7xuj_33471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_2025/7xuj_33471.map" model { file = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_2025/7xuj_33471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_2025/7xuj_33471.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 40 5.16 5 C 7486 2.51 5 N 1798 2.21 5 O 1972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11296 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5486 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 31, 'TRANS': 671} Chain breaks: 1 Chain: "B" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5486 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 31, 'TRANS': 671} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'I2R': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'I2R': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.03, per 1000 atoms: 0.62 Number of scatterers: 11296 At special positions: 0 Unit cell: (100.161, 123.855, 105.546, 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 40 16.00 O 1972 8.00 N 1798 7.00 C 7486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 62.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.668A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.630A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 72 through 95 removed outlier: 3.925A pdb=" N VAL A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.899A pdb=" N LEU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.652A pdb=" N LEU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 170 through 196 removed outlier: 3.551A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.606A pdb=" N LEU A 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.524A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 252 removed outlier: 3.545A pdb=" N LYS A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.556A pdb=" N THR A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 282 removed outlier: 3.738A pdb=" N GLN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.964A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 467 through 503 removed outlier: 6.849A pdb=" N LEU A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N GLY A 485 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 584 removed outlier: 3.625A pdb=" N GLN A 584 " --> pdb=" O LYS A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 618 removed outlier: 3.838A pdb=" N VAL A 615 " --> pdb=" O GLN A 612 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 676 Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.644A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 712 through 725 removed outlier: 3.722A pdb=" N ASP A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 25 removed outlier: 3.668A pdb=" N ASN B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.630A pdb=" N LYS B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.925A pdb=" N VAL B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.900A pdb=" N LEU B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.653A pdb=" N LEU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 Processing helix chain 'B' and resid 170 through 196 removed outlier: 3.552A pdb=" N VAL B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.606A pdb=" N LEU B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.524A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.546A pdb=" N LYS B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.555A pdb=" N THR B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 282 removed outlier: 3.739A pdb=" N GLN B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.964A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 467 through 503 removed outlier: 6.849A pdb=" N LEU B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N GLY B 485 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 584 removed outlier: 3.625A pdb=" N GLN B 584 " --> pdb=" O LYS B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 618 removed outlier: 3.839A pdb=" N VAL B 615 " --> pdb=" O GLN B 612 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 676 Processing helix chain 'B' and resid 687 through 695 removed outlier: 3.643A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 698 No H-bonds generated for 'chain 'B' and resid 696 through 698' Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 712 through 725 removed outlier: 3.723A pdb=" N ASP B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.637A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.637A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1716 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: 3.56 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1764 1.27 - 1.40: 2742 1.40 - 1.54: 6638 1.54 - 1.67: 358 1.67 - 1.81: 60 Bond restraints: 11562 Sorted by residual: bond pdb=" C10 I2R A 801 " pdb=" C5 I2R A 801 " ideal model delta sigma weight residual 1.392 1.554 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C10 I2R B 803 " pdb=" C5 I2R B 803 " ideal model delta sigma weight residual 1.392 1.554 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" C11 I2R A 801 " pdb=" C6 I2R A 801 " ideal model delta sigma weight residual 1.397 1.557 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C11 I2R B 803 " pdb=" C6 I2R B 803 " ideal model delta sigma weight residual 1.397 1.556 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" C17 I2R B 803 " pdb=" C20 I2R B 803 " ideal model delta sigma weight residual 1.389 1.533 -0.144 2.00e-02 2.50e+03 5.15e+01 ... (remaining 11557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 15480 3.06 - 6.13: 222 6.13 - 9.19: 30 9.19 - 12.25: 4 12.25 - 15.31: 2 Bond angle restraints: 15738 Sorted by residual: angle pdb=" CB GLU B 692 " pdb=" CG GLU B 692 " pdb=" CD GLU B 692 " ideal model delta sigma weight residual 112.60 122.38 -9.78 1.70e+00 3.46e-01 3.31e+01 angle pdb=" CB GLU A 692 " pdb=" CG GLU A 692 " pdb=" CD GLU A 692 " ideal model delta sigma weight residual 112.60 122.35 -9.75 1.70e+00 3.46e-01 3.29e+01 angle pdb=" CA GLU A 692 " pdb=" CB GLU A 692 " pdb=" CG GLU A 692 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA GLU B 692 " pdb=" CB GLU B 692 " pdb=" CG GLU B 692 " ideal model delta sigma weight residual 114.10 123.78 -9.68 2.00e+00 2.50e-01 2.34e+01 angle pdb=" C PRO B 287 " pdb=" N VAL B 288 " pdb=" CA VAL B 288 " ideal model delta sigma weight residual 122.13 130.42 -8.29 1.85e+00 2.92e-01 2.01e+01 ... (remaining 15733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 6418 15.26 - 30.51: 652 30.51 - 45.77: 158 45.77 - 61.03: 40 61.03 - 76.28: 6 Dihedral angle restraints: 7274 sinusoidal: 3200 harmonic: 4074 Sorted by residual: dihedral pdb=" CA THR A 238 " pdb=" C THR A 238 " pdb=" N ASP A 239 " pdb=" CA ASP A 239 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA THR B 238 " pdb=" C THR B 238 " pdb=" N ASP B 239 " pdb=" CA ASP B 239 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP B 239 " pdb=" C ASP B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta harmonic sigma weight residual 180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 7271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1808 0.119 - 0.238: 64 0.238 - 0.356: 2 0.356 - 0.475: 0 0.475 - 0.594: 2 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CB VAL B 288 " pdb=" CA VAL B 288 " pdb=" CG1 VAL B 288 " pdb=" CG2 VAL B 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" CB VAL B 641 " pdb=" CA VAL B 641 " pdb=" CG1 VAL B 641 " pdb=" CG2 VAL B 641 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1873 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 590 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO A 591 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 590 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 591 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 100 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO B 101 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " 0.035 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2767 2.79 - 3.32: 9916 3.32 - 3.84: 18134 3.84 - 4.37: 21637 4.37 - 4.90: 37355 Nonbonded interactions: 89809 Sorted by model distance: nonbonded pdb=" O LEU B 269 " pdb=" OG SER B 273 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 269 " pdb=" OG SER A 273 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR B 365 " pdb=" OE2 GLU B 404 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 365 " pdb=" OE2 GLU A 404 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR A 503 " pdb=" OH TYR A 545 " model vdw 2.313 3.040 ... (remaining 89804 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 725 or resid 802 or resid 804 through 805)) selection = (chain 'B' and (resid 8 through 725 or resid 802 or resid 804 through 805)) } 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: 0.710 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.780 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.162 11562 Z= 0.452 Angle : 0.944 15.315 15738 Z= 0.514 Chirality : 0.057 0.594 1876 Planarity : 0.008 0.080 1920 Dihedral : 13.427 76.283 4642 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.82 % Allowed : 4.95 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.17), residues: 1398 helix: -2.21 (0.13), residues: 858 sheet: 1.05 (0.81), residues: 36 loop : -2.78 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.007 0.001 HIS A 38 PHE 0.027 0.002 PHE A 130 TYR 0.026 0.002 TYR B 9 ARG 0.004 0.001 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.15286 ( 588) hydrogen bonds : angle 6.09939 ( 1716) covalent geometry : bond 0.01001 (11562) covalent geometry : angle 0.94403 (15738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.194 Fit side-chains REVERT: A 58 PHE cc_start: 0.7679 (m-80) cc_final: 0.7458 (m-80) REVERT: A 99 ASP cc_start: 0.7729 (t0) cc_final: 0.7476 (t0) REVERT: A 281 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7119 (mmm-85) REVERT: B 58 PHE cc_start: 0.7611 (m-80) cc_final: 0.7407 (m-80) REVERT: B 99 ASP cc_start: 0.7858 (t0) cc_final: 0.7561 (t0) REVERT: B 281 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7069 (mmm-85) REVERT: B 612 GLN cc_start: 0.8532 (mt0) cc_final: 0.8164 (mt0) outliers start: 22 outliers final: 4 residues processed: 151 average time/residue: 1.0423 time to fit residues: 172.9453 Evaluate side-chains 94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.076255 restraints weight = 15280.118| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.19 r_work: 0.2662 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11562 Z= 0.131 Angle : 0.610 15.792 15738 Z= 0.317 Chirality : 0.042 0.150 1876 Planarity : 0.005 0.067 1920 Dihedral : 8.071 94.826 2094 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.16 % Allowed : 8.91 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1398 helix: -0.10 (0.17), residues: 882 sheet: 1.56 (0.82), residues: 36 loop : -2.18 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.008 0.001 HIS B 31 PHE 0.021 0.001 PHE B 627 TYR 0.009 0.001 TYR B 107 ARG 0.007 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 588) hydrogen bonds : angle 4.15281 ( 1716) covalent geometry : bond 0.00290 (11562) covalent geometry : angle 0.61012 (15738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.178 Fit side-chains REVERT: A 58 PHE cc_start: 0.7450 (m-80) cc_final: 0.7153 (m-80) REVERT: A 281 ARG cc_start: 0.7408 (ttm-80) cc_final: 0.7024 (mmm-85) REVERT: B 24 ASN cc_start: 0.9081 (m-40) cc_final: 0.8734 (m110) REVERT: B 58 PHE cc_start: 0.7542 (m-80) cc_final: 0.7254 (m-80) REVERT: B 99 ASP cc_start: 0.8615 (t0) cc_final: 0.8414 (t0) REVERT: B 281 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.6995 (mmm-85) REVERT: B 529 MET cc_start: 0.9116 (mmm) cc_final: 0.8868 (mmt) outliers start: 14 outliers final: 7 residues processed: 112 average time/residue: 1.0183 time to fit residues: 126.3295 Evaluate side-chains 100 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 628 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.076323 restraints weight = 15431.456| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.21 r_work: 0.2651 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.123 Angle : 0.589 15.716 15738 Z= 0.304 Chirality : 0.042 0.151 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.334 59.251 2090 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.06 % Allowed : 8.83 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1398 helix: 0.62 (0.19), residues: 868 sheet: 1.67 (0.83), residues: 36 loop : -2.02 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.015 0.002 HIS B 31 PHE 0.018 0.001 PHE A 130 TYR 0.009 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 588) hydrogen bonds : angle 3.93985 ( 1716) covalent geometry : bond 0.00271 (11562) covalent geometry : angle 0.58862 (15738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.368 Fit side-chains REVERT: A 38 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7312 (m-70) REVERT: A 58 PHE cc_start: 0.7453 (m-80) cc_final: 0.7137 (m-80) REVERT: A 281 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.7043 (mmm-85) REVERT: B 18 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8958 (m) REVERT: B 24 ASN cc_start: 0.9088 (m-40) cc_final: 0.8703 (m110) REVERT: B 26 LYS cc_start: 0.8530 (ptmm) cc_final: 0.8297 (ptmt) REVERT: B 38 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7301 (m-70) REVERT: B 58 PHE cc_start: 0.7497 (m-80) cc_final: 0.7203 (m-80) REVERT: B 99 ASP cc_start: 0.8595 (t0) cc_final: 0.8395 (t0) REVERT: B 281 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7064 (mmm-85) REVERT: B 529 MET cc_start: 0.9121 (mmm) cc_final: 0.8877 (mmt) REVERT: B 698 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8193 (mp0) outliers start: 25 outliers final: 12 residues processed: 115 average time/residue: 1.0167 time to fit residues: 130.5018 Evaluate side-chains 107 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 42 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 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 = 0.3358 r_free = 0.3358 target = 0.113394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.076562 restraints weight = 15355.390| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.20 r_work: 0.2673 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.123 Angle : 0.589 15.716 15738 Z= 0.304 Chirality : 0.042 0.151 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.761 118.116 2090 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.24 % Allowed : 10.89 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1398 helix: 0.62 (0.19), residues: 868 sheet: 1.67 (0.83), residues: 36 loop : -2.02 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.015 0.002 HIS B 31 PHE 0.018 0.001 PHE A 130 TYR 0.009 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 588) hydrogen bonds : angle 3.93985 ( 1716) covalent geometry : bond 0.00271 (11562) covalent geometry : angle 0.58862 (15738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.280 Fit side-chains REVERT: A 38 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7307 (m-70) REVERT: A 58 PHE cc_start: 0.7465 (m-80) cc_final: 0.7150 (m-80) REVERT: A 281 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7044 (mmm-85) REVERT: B 18 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8952 (m) REVERT: B 24 ASN cc_start: 0.9090 (m-40) cc_final: 0.8710 (m110) REVERT: B 26 LYS cc_start: 0.8536 (ptmm) cc_final: 0.8310 (ptmt) REVERT: B 38 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7296 (m-70) REVERT: B 58 PHE cc_start: 0.7515 (m-80) cc_final: 0.7222 (m-80) REVERT: B 281 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7057 (mmm-85) REVERT: B 529 MET cc_start: 0.9123 (mmm) cc_final: 0.8875 (mmt) REVERT: B 698 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8200 (mp0) outliers start: 15 outliers final: 12 residues processed: 100 average time/residue: 1.6858 time to fit residues: 184.4879 Evaluate side-chains 104 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 104 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.114630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.077979 restraints weight = 15302.288| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.20 r_work: 0.2692 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11562 Z= 0.109 Angle : 0.581 17.167 15738 Z= 0.295 Chirality : 0.042 0.162 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.461 96.442 2090 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.65 % Allowed : 11.22 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1398 helix: 1.01 (0.19), residues: 864 sheet: 1.78 (0.84), residues: 36 loop : -1.85 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.002 0.001 HIS A 31 PHE 0.017 0.001 PHE A 130 TYR 0.006 0.001 TYR B 9 ARG 0.004 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 588) hydrogen bonds : angle 3.79501 ( 1716) covalent geometry : bond 0.00233 (11562) covalent geometry : angle 0.58098 (15738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 2.713 Fit side-chains REVERT: A 26 LYS cc_start: 0.8852 (pmmt) cc_final: 0.8476 (ptmt) REVERT: A 38 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7276 (m-70) REVERT: A 48 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7722 (mp10) REVERT: A 58 PHE cc_start: 0.7383 (m-80) cc_final: 0.7074 (m-80) REVERT: A 281 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.7033 (mmm-85) REVERT: B 18 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8954 (m) REVERT: B 24 ASN cc_start: 0.9071 (m-40) cc_final: 0.8681 (m110) REVERT: B 38 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7322 (m-70) REVERT: B 58 PHE cc_start: 0.7533 (m-80) cc_final: 0.7269 (m-80) REVERT: B 70 LYS cc_start: 0.8950 (tptt) cc_final: 0.8574 (tppp) REVERT: B 281 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7070 (mmm-85) outliers start: 20 outliers final: 10 residues processed: 111 average time/residue: 1.4257 time to fit residues: 175.7078 Evaluate side-chains 104 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.077777 restraints weight = 15545.216| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.23 r_work: 0.2683 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11562 Z= 0.117 Angle : 0.591 17.438 15738 Z= 0.301 Chirality : 0.042 0.168 1876 Planarity : 0.004 0.062 1920 Dihedral : 7.573 115.633 2090 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.57 % Allowed : 12.46 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1398 helix: 1.08 (0.19), residues: 866 sheet: 1.80 (0.85), residues: 36 loop : -1.80 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS B 32 PHE 0.017 0.001 PHE A 130 TYR 0.007 0.001 TYR B 9 ARG 0.003 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 588) hydrogen bonds : angle 3.78677 ( 1716) covalent geometry : bond 0.00252 (11562) covalent geometry : angle 0.59061 (15738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.346 Fit side-chains REVERT: A 24 ASN cc_start: 0.8944 (m-40) cc_final: 0.8458 (m110) REVERT: A 26 LYS cc_start: 0.8832 (pmmt) cc_final: 0.8437 (ptmt) REVERT: A 38 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7256 (m-70) REVERT: A 48 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7661 (mp10) REVERT: A 58 PHE cc_start: 0.7324 (m-80) cc_final: 0.7010 (m-80) REVERT: A 281 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7075 (mmm-85) REVERT: B 18 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8945 (m) REVERT: B 24 ASN cc_start: 0.9073 (m-40) cc_final: 0.8668 (m110) REVERT: B 26 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8213 (pmmt) REVERT: B 38 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7304 (m-70) REVERT: B 58 PHE cc_start: 0.7477 (m-80) cc_final: 0.7208 (m-80) REVERT: B 70 LYS cc_start: 0.8959 (tptt) cc_final: 0.8583 (tppp) REVERT: B 281 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.7070 (mmm-85) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 1.3860 time to fit residues: 159.0914 Evaluate side-chains 107 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 104 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 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 = 0.3371 r_free = 0.3371 target = 0.114528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.077829 restraints weight = 15547.503| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.22 r_work: 0.2675 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11562 Z= 0.117 Angle : 0.591 17.438 15738 Z= 0.301 Chirality : 0.042 0.168 1876 Planarity : 0.004 0.062 1920 Dihedral : 7.594 118.116 2090 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.24 % Allowed : 12.54 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1398 helix: 1.08 (0.19), residues: 866 sheet: 1.80 (0.85), residues: 36 loop : -1.80 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS B 32 PHE 0.017 0.001 PHE A 130 TYR 0.007 0.001 TYR B 9 ARG 0.003 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 588) hydrogen bonds : angle 3.78677 ( 1716) covalent geometry : bond 0.00253 (11562) covalent geometry : angle 0.59072 (15738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.384 Fit side-chains REVERT: A 24 ASN cc_start: 0.8949 (m-40) cc_final: 0.8468 (m110) REVERT: A 26 LYS cc_start: 0.8853 (pmmt) cc_final: 0.8473 (ptmt) REVERT: A 38 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7283 (m-70) REVERT: A 48 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7679 (mp10) REVERT: A 58 PHE cc_start: 0.7371 (m-80) cc_final: 0.7058 (m-80) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7107 (mmm-85) REVERT: B 18 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8962 (m) REVERT: B 24 ASN cc_start: 0.9080 (m-40) cc_final: 0.8689 (m110) REVERT: B 26 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8257 (pmmt) REVERT: B 38 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7325 (m-70) REVERT: B 58 PHE cc_start: 0.7529 (m-80) cc_final: 0.7262 (m-80) REVERT: B 70 LYS cc_start: 0.8963 (tptt) cc_final: 0.8590 (tppp) REVERT: B 281 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7102 (mmm-85) outliers start: 15 outliers final: 12 residues processed: 100 average time/residue: 1.0258 time to fit residues: 114.1897 Evaluate side-chains 107 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 1 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.114711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.078010 restraints weight = 15466.877| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.23 r_work: 0.2685 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11562 Z= 0.113 Angle : 0.594 18.906 15738 Z= 0.300 Chirality : 0.042 0.149 1876 Planarity : 0.004 0.062 1920 Dihedral : 7.512 111.856 2090 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.82 % Allowed : 12.05 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1398 helix: 1.15 (0.19), residues: 866 sheet: 1.84 (0.85), residues: 36 loop : -1.74 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.002 0.001 HIS A 25 PHE 0.017 0.001 PHE A 130 TYR 0.006 0.001 TYR B 367 ARG 0.003 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 588) hydrogen bonds : angle 3.76832 ( 1716) covalent geometry : bond 0.00246 (11562) covalent geometry : angle 0.59414 (15738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.192 Fit side-chains REVERT: A 26 LYS cc_start: 0.8828 (pmmt) cc_final: 0.8465 (ptmt) REVERT: A 38 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7251 (m-70) REVERT: A 48 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7665 (mp10) REVERT: A 58 PHE cc_start: 0.7313 (m-80) cc_final: 0.6994 (m-80) REVERT: A 259 ILE cc_start: 0.8561 (pp) cc_final: 0.8184 (mp) REVERT: A 281 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.7043 (mmm-85) REVERT: B 18 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8956 (m) REVERT: B 24 ASN cc_start: 0.9070 (m-40) cc_final: 0.8666 (m110) REVERT: B 26 LYS cc_start: 0.8588 (ptmm) cc_final: 0.8216 (pmmt) REVERT: B 38 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7298 (m-70) REVERT: B 58 PHE cc_start: 0.7462 (m-80) cc_final: 0.7189 (m-80) REVERT: B 70 LYS cc_start: 0.8970 (tptt) cc_final: 0.8588 (tppp) REVERT: B 276 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8108 (mttm) REVERT: B 281 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7064 (mmm-85) REVERT: B 293 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6767 (mp0) outliers start: 22 outliers final: 13 residues processed: 107 average time/residue: 0.9823 time to fit residues: 116.6075 Evaluate side-chains 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.077938 restraints weight = 15451.241| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.21 r_work: 0.2688 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11562 Z= 0.115 Angle : 0.592 18.916 15738 Z= 0.298 Chirality : 0.042 0.145 1876 Planarity : 0.004 0.062 1920 Dihedral : 7.617 118.106 2090 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.40 % Allowed : 12.38 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1398 helix: 1.15 (0.19), residues: 866 sheet: 1.84 (0.85), residues: 36 loop : -1.74 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.002 0.001 HIS A 32 PHE 0.017 0.001 PHE A 130 TYR 0.006 0.001 TYR B 367 ARG 0.003 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 588) hydrogen bonds : angle 3.76816 ( 1716) covalent geometry : bond 0.00248 (11562) covalent geometry : angle 0.59210 (15738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.218 Fit side-chains REVERT: A 26 LYS cc_start: 0.8851 (pmmt) cc_final: 0.8504 (ptmt) REVERT: A 38 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7272 (m-70) REVERT: A 48 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7681 (mp10) REVERT: A 58 PHE cc_start: 0.7366 (m-80) cc_final: 0.7050 (m-80) REVERT: A 259 ILE cc_start: 0.8607 (pp) cc_final: 0.8229 (mp) REVERT: A 281 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.7069 (mmm-85) REVERT: B 18 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8973 (m) REVERT: B 24 ASN cc_start: 0.9079 (m-40) cc_final: 0.8692 (m110) REVERT: B 26 LYS cc_start: 0.8606 (ptmm) cc_final: 0.8267 (pmmt) REVERT: B 38 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7317 (m-70) REVERT: B 58 PHE cc_start: 0.7520 (m-80) cc_final: 0.7248 (m-80) REVERT: B 70 LYS cc_start: 0.8971 (tptt) cc_final: 0.8594 (tppp) REVERT: B 276 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8150 (mttm) REVERT: B 281 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.7099 (mmm-85) REVERT: B 293 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6803 (mp0) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 1.0548 time to fit residues: 116.9600 Evaluate side-chains 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 131 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 3 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 96 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.078882 restraints weight = 15425.880| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.21 r_work: 0.2714 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11562 Z= 0.112 Angle : 0.591 19.170 15738 Z= 0.296 Chirality : 0.042 0.153 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.023 57.373 2088 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.40 % Allowed : 12.46 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1398 helix: 1.40 (0.19), residues: 854 sheet: 1.96 (0.87), residues: 36 loop : -1.64 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 63 HIS 0.002 0.001 HIS B 220 PHE 0.020 0.001 PHE B 282 TYR 0.006 0.001 TYR B 545 ARG 0.004 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 588) hydrogen bonds : angle 3.71473 ( 1716) covalent geometry : bond 0.00243 (11562) covalent geometry : angle 0.59099 (15738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.262 Fit side-chains REVERT: A 26 LYS cc_start: 0.8868 (pmmt) cc_final: 0.8502 (ptmt) REVERT: A 38 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7339 (m-70) REVERT: A 48 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7655 (mp10) REVERT: A 58 PHE cc_start: 0.7340 (m-80) cc_final: 0.7033 (m-80) REVERT: A 281 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.7030 (mmm-85) REVERT: B 18 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8982 (m) REVERT: B 24 ASN cc_start: 0.9080 (m-40) cc_final: 0.8718 (m110) REVERT: B 26 LYS cc_start: 0.8633 (ptmm) cc_final: 0.8309 (pmmt) REVERT: B 38 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7430 (m-70) REVERT: B 48 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7851 (mp10) REVERT: B 58 PHE cc_start: 0.7483 (m-80) cc_final: 0.7209 (m-80) REVERT: B 70 LYS cc_start: 0.8929 (tptt) cc_final: 0.8546 (tppp) REVERT: B 281 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7048 (mtp180) REVERT: B 329 ILE cc_start: 0.8883 (pt) cc_final: 0.8471 (pp) outliers start: 17 outliers final: 8 residues processed: 105 average time/residue: 1.0590 time to fit residues: 123.4521 Evaluate side-chains 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 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 = 0.3384 r_free = 0.3384 target = 0.115445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.078938 restraints weight = 15314.337| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.20 r_work: 0.2694 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11562 Z= 0.112 Angle : 0.591 19.170 15738 Z= 0.296 Chirality : 0.042 0.153 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.023 57.373 2088 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.91 % Allowed : 13.04 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1398 helix: 1.40 (0.19), residues: 854 sheet: 1.96 (0.87), residues: 36 loop : -1.64 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 63 HIS 0.002 0.001 HIS B 220 PHE 0.020 0.001 PHE B 282 TYR 0.006 0.001 TYR B 545 ARG 0.004 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 588) hydrogen bonds : angle 3.71473 ( 1716) covalent geometry : bond 0.00243 (11562) covalent geometry : angle 0.59100 (15738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8309.60 seconds wall clock time: 152 minutes 47.77 seconds (9167.77 seconds total)