Starting phenix.real_space_refine
on Tue Feb 11 17:37:28 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7xvg_33486/02_2025/7xvg_33486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xvg_33486/02_2025/7xvg_33486.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xvg_33486/02_2025/7xvg_33486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xvg_33486/02_2025/7xvg_33486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xvg_33486/02_2025/7xvg_33486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xvg_33486/02_2025/7xvg_33486.cif"
  }
  resolution = 3.6
  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=   0.001 sd=   0.047
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      26      5.16       5
     C    4160      2.51       5
     N    1066      2.21       5
     O    1186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6438
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3327
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 20, 'TRANS': 394}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 3111
          Classifications: {'peptide': 379}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 368}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 4.06, per 1000 atoms: 0.63
  Number of scatterers: 6438
  At special positions: 0
  Unit cell: (75.6, 94.08, 110.04, 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      26     16.00
     O    1186      8.00
     N    1066      7.00
     C    4160      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: 1.51
  Conformation dependent library (CDL) restraints added in 841.3 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1510

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      50.5% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 434 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 469 through 482
    Processing helix  chain 'A' and resid 502 through 514
      removed outlier: 3.835A  pdb=" N   ASP A 507 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LEU A 508 " --> pdb=" O   MET A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 598
      removed outlier: 3.532A  pdb=" N   LEU A 598 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 621
      removed outlier: 3.701A  pdb=" N   ILE A 618 " --> pdb=" O   PRO A 615 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   GLY A 619 " --> pdb=" O   MET A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 665
    Processing helix  chain 'A' and resid 680 through 687
      removed outlier: 3.672A  pdb=" N   VAL A 684 " --> pdb=" O   ASP A 680 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A 687 " --> pdb=" O   PHE A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 690
      No H-bonds generated for 'chain 'A' and resid 688 through 690'
    Processing helix  chain 'A' and resid 707 through 718
      removed outlier: 4.170A  pdb=" N   LEU A 711 " --> pdb=" O   MET A 707 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU A 713 " --> pdb=" O   LYS A 709 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   SER A 716 " --> pdb=" O   GLU A 712 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   MET A 718 " --> pdb=" O   SER A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 792
    Processing helix  chain 'A' and resid 804 through 810
      removed outlier: 3.833A  pdb=" N   PHE A 808 " --> pdb=" O   ASN A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 844
      removed outlier: 3.719A  pdb=" N   PHE A 844 " --> pdb=" O   PRO A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 864
      removed outlier: 3.795A  pdb=" N   ILE A 864 " --> pdb=" O   ALA A 861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 150
      removed outlier: 4.252A  pdb=" N   TYR B 148 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 193
      removed outlier: 3.560A  pdb=" N   ASN B 189 " --> pdb=" O   PHE B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
      removed outlier: 4.365A  pdb=" N   ILE B 198 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LEU B 199 " --> pdb=" O   ASP B 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 194 through 199'
    Processing helix  chain 'B' and resid 211 through 226
    Processing helix  chain 'B' and resid 229 through 244
      removed outlier: 3.984A  pdb=" N   ILE B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   GLU B 235 " --> pdb=" O   GLU B 231 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL B 240 " --> pdb=" O   GLU B 236 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LYS B 243 " --> pdb=" O   LYS B 239 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL B 244 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 275
      removed outlier: 3.552A  pdb=" N   ILE B 262 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN B 263 " --> pdb=" O   ASN B 259 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE B 270 " --> pdb=" O   ALA B 266 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   HIS B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS B 275 " --> pdb=" O   HIS B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 289
    Processing helix  chain 'B' and resid 290 through 317
      removed outlier: 3.530A  pdb=" N   LYS B 295 " --> pdb=" O   ASP B 291 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS B 308 " --> pdb=" O   THR B 304 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   PHE B 310 " --> pdb=" O   LYS B 306 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   ASP B 311 " --> pdb=" O   MET B 307 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   SER B 312 " --> pdb=" O   LYS B 308 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LYS B 315 " --> pdb=" O   ASP B 311 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   MET B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 322
      removed outlier: 3.680A  pdb=" N   ILE B 322 " --> pdb=" O   ASN B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 330
      removed outlier: 4.281A  pdb=" N   ASP B 328 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 329 " --> pdb=" O   MET B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
      removed outlier: 3.565A  pdb=" N   SER B 334 " --> pdb=" O   TRP B 331 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   HIS B 335 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 331 through 335'
    Processing helix  chain 'B' and resid 336 through 347
      removed outlier: 4.094A  pdb=" N   LEU B 343 " --> pdb=" O   PHE B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 365
      removed outlier: 3.835A  pdb=" N   SER B 351 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER B 352 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 392
    Processing helix  chain 'B' and resid 393 through 396
    Processing helix  chain 'B' and resid 403 through 419
    Processing helix  chain 'B' and resid 423 through 441
      removed outlier: 3.597A  pdb=" N   PHE B 441 " --> pdb=" O   LEU B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 455
      removed outlier: 3.757A  pdb=" N   LEU B 452 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 483
    Processing helix  chain 'B' and resid 508 through 529
      removed outlier: 4.253A  pdb=" N   LYS B 512 " --> pdb=" O   LYS B 508 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLU B 513 " --> pdb=" O   HIS B 509 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   VAL B 516 " --> pdb=" O   LYS B 512 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   SER B 517 " --> pdb=" O   GLU B 513 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR B 518 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ARG B 529 " --> pdb=" O   THR B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 553
      removed outlier: 3.556A  pdb=" N   LEU B 544 " --> pdb=" O   CYS B 540 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER B 553 " --> pdb=" O   ASN B 549 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 445
      removed outlier: 6.538A  pdb=" N   VAL A 496 " --> pdb=" O   ILE A 490 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   ILE A 490 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG A 500 " --> pdb=" O   GLN A 486 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLN A 486 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 583
    Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 628
      removed outlier: 6.848A  pdb=" N   LEU A 627 " --> pdb=" O   TYR A 651 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ASP A 672 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   ARG A 697 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP A 699 " --> pdb=" O   LEU A 674 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ASP A 725 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 799 through 802
      removed outlier: 7.512A  pdb=" N   LEU A 800 " --> pdb=" O   ARG A 833 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 856 through 859
      removed outlier: 3.857A  pdb=" N   PHE A 857 " --> pdb=" O   ARG A 881 " (cutoff:3.500A)

    230 hydrogen bonds defined for protein.
    645 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.79 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 1132
        1.32 -     1.44: 1657
        1.44 -     1.57: 3744
        1.57 -     1.69: 1
        1.69 -     1.81: 42
  Bond restraints: 6576
  Sorted by residual:
  bond pdb=" N   LEU A 879 "
       pdb=" CA  LEU A 879 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.036 1.36e-02 5.41e+03 6.95e+00
  bond pdb=" C   PRO A 877 "
       pdb=" O   PRO A 877 "
    ideal  model  delta    sigma   weight residual
    1.235  1.203  0.032 1.30e-02 5.92e+03 6.21e+00
  bond pdb=" N   SER A 878 "
       pdb=" CA  SER A 878 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.11e+00
  bond pdb=" CA  SER A 878 "
       pdb=" CB  SER A 878 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.042 1.69e-02 3.50e+03 6.11e+00
  bond pdb=" N   LEU A 690 "
       pdb=" CA  LEU A 690 "
    ideal  model  delta    sigma   weight residual
    1.462  1.490 -0.028 1.23e-02 6.61e+03 5.05e+00
  ... (remaining 6571 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 8666
        2.05 -     4.10: 179
        4.10 -     6.15: 28
        6.15 -     8.19: 6
        8.19 -    10.24: 3
  Bond angle restraints: 8882
  Sorted by residual:
  angle pdb=" N   ILE B 318 "
        pdb=" CA  ILE B 318 "
        pdb=" C   ILE B 318 "
      ideal   model   delta    sigma   weight residual
     111.91  108.20    3.71 8.90e-01 1.26e+00 1.73e+01
  angle pdb=" N   GLU A 478 "
        pdb=" CA  GLU A 478 "
        pdb=" CB  GLU A 478 "
      ideal   model   delta    sigma   weight residual
     110.28  116.49   -6.21 1.55e+00 4.16e-01 1.61e+01
  angle pdb=" N   ARG A 689 "
        pdb=" CA  ARG A 689 "
        pdb=" C   ARG A 689 "
      ideal   model   delta    sigma   weight residual
     112.89  108.19    4.70 1.24e+00 6.50e-01 1.43e+01
  angle pdb=" C   ASN A 477 "
        pdb=" N   GLU A 478 "
        pdb=" CA  GLU A 478 "
      ideal   model   delta    sigma   weight residual
     120.31  115.12    5.19 1.52e+00 4.33e-01 1.17e+01
  angle pdb=" C   PRO A 850 "
        pdb=" N   ARG A 851 "
        pdb=" CA  ARG A 851 "
      ideal   model   delta    sigma   weight residual
     122.56  117.89    4.67 1.50e+00 4.44e-01 9.71e+00
  ... (remaining 8877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3547
       17.95 -    35.90: 360
       35.90 -    53.86: 45
       53.86 -    71.81: 10
       71.81 -    89.76: 5
  Dihedral angle restraints: 3967
    sinusoidal: 1638
      harmonic: 2329
  Sorted by residual:
  dihedral pdb=" CA  LEU A 693 "
           pdb=" C   LEU A 693 "
           pdb=" N   ARG A 694 "
           pdb=" CA  ARG A 694 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.18   20.82     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CG  ARG A 689 "
           pdb=" CD  ARG A 689 "
           pdb=" NE  ARG A 689 "
           pdb=" CZ  ARG A 689 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -32.90  -57.10     2      1.50e+01 4.44e-03 1.50e+01
  dihedral pdb=" CA  LEU B 267 "
           pdb=" C   LEU B 267 "
           pdb=" N   GLN B 268 "
           pdb=" CA  GLN B 268 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.84   17.16     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 3964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 761
       0.052 -    0.103: 195
       0.103 -    0.155: 37
       0.155 -    0.207: 0
       0.207 -    0.259: 3
  Chirality restraints: 996
  Sorted by residual:
  chirality pdb=" CA  ARG A 689 "
            pdb=" N   ARG A 689 "
            pdb=" C   ARG A 689 "
            pdb=" CB  ARG A 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CB  ILE A 869 "
            pdb=" CA  ILE A 869 "
            pdb=" CG1 ILE A 869 "
            pdb=" CG2 ILE A 869 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  LEU A 879 "
            pdb=" N   LEU A 879 "
            pdb=" C   LEU A 879 "
            pdb=" CB  LEU A 879 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 993 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 688 "   -0.020 2.00e-02 2.50e+03   4.00e-02 1.60e+01
        pdb=" C   GLY A 688 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLY A 688 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ARG A 689 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 876 "    0.018 2.00e-02 2.50e+03   3.51e-02 1.24e+01
        pdb=" C   LEU A 876 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   LEU A 876 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PRO A 877 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 689 "   -0.161 9.50e-02 1.11e+02   7.23e-02 3.21e+00
        pdb=" NE  ARG A 689 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 689 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 689 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 689 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 84
        2.64 -     3.20: 6170
        3.20 -     3.77: 9567
        3.77 -     4.33: 12956
        4.33 -     4.90: 20683
  Nonbonded interactions: 49460
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A 879 "
            pdb=" N   GLN A 880 "
     model   vdw
     2.074 3.540
  nonbonded pdb=" O   THR A 691 "
            pdb=" OG1 THR A 691 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   GLU B 222 "
            pdb=" OG1 THR B 226 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG  SER A 842 "
            pdb=" O   ASN A 868 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   GLU A 713 "
            pdb=" OG  SER A 716 "
     model   vdw
     2.265 3.040
  ... (remaining 49455 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.650
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
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      :  0.004   0.055   6576  Z= 0.243
  Angle     :  0.728  10.242   8882  Z= 0.381
  Chirality :  0.048   0.259    996
  Planarity :  0.005   0.072   1116
  Dihedral  : 14.260  89.760   2457
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.90 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.83 %
    Favored  : 98.90 %
  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: -0.97 (0.31), residues: 780
  helix:  0.51 (0.30), residues: 325
  sheet: -2.62 (0.73), residues: 59
  loop : -1.30 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 856 
 HIS   0.005   0.001   HIS B 359 
 PHE   0.028   0.002   PHE B 233 
 TYR   0.015   0.001   TYR A 460 
 ARG   0.003   0.000   ARG A 500 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 GLN cc_start: 0.8144 (pm20) cc_final: 0.7928 (pm20)
REVERT: B  195 ASP cc_start: 0.8268 (m-30) cc_final: 0.7995 (t0)
REVERT: B  501 PHE cc_start: 0.7888 (m-80) cc_final: 0.7556 (m-80)
REVERT: B  516 VAL cc_start: 0.8205 (t) cc_final: 0.7780 (t)
  outliers start: 2
  outliers final: 2
  residues processed: 107
  average time/residue: 0.1772
  time to fit residues: 26.1240
Evaluate side-chains
  87 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 ARG
Chi-restraints excluded: chain A residue  691 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0070
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.5598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 729 ASN
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.155896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.122675 restraints weight = 11197.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.123898 restraints weight = 6243.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.124913 restraints weight = 5317.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6576  Z= 0.179
  Angle     :  0.654  10.200   8882  Z= 0.317
  Chirality :  0.044   0.138    996
  Planarity :  0.004   0.041   1116
  Dihedral  :  4.884  57.474    859
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.76 %
    Favored  : 88.41 %
  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: -1.01 (0.30), residues: 780
  helix:  0.52 (0.29), residues: 333
  sheet: -2.74 (0.69), residues: 61
  loop : -1.38 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 453 
 HIS   0.007   0.001   HIS A 502 
 PHE   0.021   0.001   PHE A 703 
 TYR   0.014   0.001   TYR B 383 
 ARG   0.003   0.000   ARG A 448 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 ILE cc_start: 0.6955 (tp) cc_final: 0.6705 (tp)
REVERT: A  669 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6747 (tm-30)
REVERT: A  682 ASP cc_start: 0.8268 (p0) cc_final: 0.7724 (p0)
REVERT: A  809 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7985 (mm-30)
REVERT: B  195 ASP cc_start: 0.8431 (m-30) cc_final: 0.8161 (t0)
REVERT: B  233 PHE cc_start: 0.7369 (t80) cc_final: 0.7123 (t80)
REVERT: B  501 PHE cc_start: 0.7988 (m-80) cc_final: 0.7578 (m-10)
  outliers start: 6
  outliers final: 3
  residues processed: 100
  average time/residue: 0.1739
  time to fit residues: 24.0390
Evaluate side-chains
  91 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    1.2782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.153641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.114764 restraints weight = 11495.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.118875 restraints weight = 6162.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.121358 restraints weight = 4305.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6576  Z= 0.214
  Angle     :  0.628   9.380   8882  Z= 0.309
  Chirality :  0.044   0.135    996
  Planarity :  0.004   0.040   1116
  Dihedral  :  4.404  18.407    854
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.83 %
    Favored  : 85.10 %
  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: -0.97 (0.31), residues: 780
  helix:  0.44 (0.29), residues: 333
  sheet: -2.67 (0.68), residues: 61
  loop : -1.25 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 453 
 HIS   0.005   0.001   HIS B 359 
 PHE   0.021   0.002   PHE A 703 
 TYR   0.014   0.001   TYR A 799 
 ARG   0.003   0.000   ARG A 448 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  585 GLU cc_start: 0.7891 (pp20) cc_final: 0.7526 (pm20)
REVERT: A  634 ILE cc_start: 0.6927 (tp) cc_final: 0.6651 (tp)
REVERT: A  682 ASP cc_start: 0.8303 (p0) cc_final: 0.7960 (p0)
REVERT: B  195 ASP cc_start: 0.8473 (m-30) cc_final: 0.8256 (t0)
REVERT: B  501 PHE cc_start: 0.7984 (m-80) cc_final: 0.7547 (m-10)
  outliers start: 15
  outliers final: 11
  residues processed: 100
  average time/residue: 0.1657
  time to fit residues: 23.4072
Evaluate side-chains
  96 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  649 CYS
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  729 ASN
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  873 MET
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 12 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.148915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.109518 restraints weight = 11505.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.113481 restraints weight = 6186.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.115958 restraints weight = 4345.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6576  Z= 0.346
  Angle     :  0.706   9.098   8882  Z= 0.355
  Chirality :  0.048   0.159    996
  Planarity :  0.004   0.047   1116
  Dihedral  :  4.733  20.341    854
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.59 %
    Favored  : 80.69 %
  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: -1.24 (0.30), residues: 780
  helix:  0.26 (0.29), residues: 334
  sheet: -3.14 (0.63), residues: 65
  loop : -1.34 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 856 
 HIS   0.007   0.001   HIS B 359 
 PHE   0.022   0.002   PHE A 703 
 TYR   0.023   0.002   TYR A 799 
 ARG   0.004   0.001   ARG A 446 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  585 GLU cc_start: 0.8046 (pp20) cc_final: 0.7331 (pm20)
REVERT: A  873 MET cc_start: 0.4077 (OUTLIER) cc_final: 0.3762 (mmm)
REVERT: B  433 GLU cc_start: 0.7999 (pt0) cc_final: 0.7747 (pt0)
REVERT: B  437 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8304 (tt)
REVERT: B  501 PHE cc_start: 0.8037 (m-80) cc_final: 0.7527 (m-10)
  outliers start: 27
  outliers final: 15
  residues processed: 112
  average time/residue: 0.1599
  time to fit residues: 25.1313
Evaluate side-chains
  100 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  729 ASN
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  873 MET
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.152137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.117591 restraints weight = 11369.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.119737 restraints weight = 6318.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.120550 restraints weight = 4961.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6576  Z= 0.194
  Angle     :  0.641   8.575   8882  Z= 0.316
  Chirality :  0.044   0.142    996
  Planarity :  0.004   0.042   1116
  Dihedral  :  4.454  21.723    854
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.21 %
    Favored  : 78.34 %
  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: -0.94 (0.31), residues: 780
  helix:  0.53 (0.29), residues: 334
  sheet: -2.94 (0.65), residues: 63
  loop : -1.21 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 356 
 HIS   0.005   0.001   HIS B 359 
 PHE   0.020   0.001   PHE A 703 
 TYR   0.015   0.001   TYR B 383 
 ARG   0.007   0.000   ARG B 186 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
REVERT: A  585 GLU cc_start: 0.7953 (pp20) cc_final: 0.7339 (pm20)
REVERT: A  873 MET cc_start: 0.4033 (OUTLIER) cc_final: 0.3821 (mmm)
REVERT: A  881 ARG cc_start: 0.6147 (tpm170) cc_final: 0.5799 (tpm170)
REVERT: B  437 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8294 (tt)
REVERT: B  472 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7642 (mm-30)
REVERT: B  501 PHE cc_start: 0.7990 (m-80) cc_final: 0.7537 (m-10)
  outliers start: 25
  outliers final: 12
  residues processed: 110
  average time/residue: 0.1609
  time to fit residues: 24.7381
Evaluate side-chains
  102 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 TRP
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  729 ASN
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  873 MET
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 39 optimal weight:    0.4980
   overall best weight:    1.4784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.151260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.118497 restraints weight = 10952.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.118120 restraints weight = 7414.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.119394 restraints weight = 7293.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6576  Z= 0.238
  Angle     :  0.644   8.199   8882  Z= 0.320
  Chirality :  0.044   0.135    996
  Planarity :  0.004   0.042   1116
  Dihedral  :  4.433  20.015    854
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.17 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.93 (0.31), residues: 780
  helix:  0.56 (0.29), residues: 334
  sheet: -3.14 (0.60), residues: 71
  loop : -1.14 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 356 
 HIS   0.009   0.001   HIS B 509 
 PHE   0.019   0.002   PHE B 233 
 TYR   0.014   0.001   TYR B 383 
 ARG   0.006   0.000   ARG B 186 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 GLU cc_start: 0.7765 (pp20) cc_final: 0.7547 (pp20)
REVERT: A  486 GLN cc_start: 0.8106 (pm20) cc_final: 0.7888 (pm20)
REVERT: A  585 GLU cc_start: 0.7875 (pp20) cc_final: 0.7406 (pm20)
REVERT: A  873 MET cc_start: 0.4529 (OUTLIER) cc_final: 0.4320 (mmm)
REVERT: A  881 ARG cc_start: 0.6510 (tpm170) cc_final: 0.6124 (tpm170)
REVERT: B  437 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8500 (tt)
REVERT: B  472 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7603 (mm-30)
REVERT: B  501 PHE cc_start: 0.7815 (m-80) cc_final: 0.7468 (m-10)
  outliers start: 24
  outliers final: 18
  residues processed: 102
  average time/residue: 0.1577
  time to fit residues: 22.6691
Evaluate side-chains
  107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  729 ASN
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  873 MET
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 59 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 12 optimal weight:    0.3980
   chunk 72 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.153173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.114555 restraints weight = 11380.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.118779 restraints weight = 6063.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.121412 restraints weight = 4226.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6576  Z= 0.168
  Angle     :  0.631   9.831   8882  Z= 0.303
  Chirality :  0.043   0.138    996
  Planarity :  0.004   0.038   1116
  Dihedral  :  4.293  21.436    854
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.31 %
    Favored  : 77.38 %
  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: -0.67 (0.31), residues: 780
  helix:  0.71 (0.29), residues: 334
  sheet: -2.72 (0.63), residues: 66
  loop : -1.02 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 356 
 HIS   0.012   0.001   HIS B 509 
 PHE   0.018   0.001   PHE B 233 
 TYR   0.014   0.001   TYR B 383 
 ARG   0.007   0.000   ARG B 186 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 LEU cc_start: 0.7923 (tt) cc_final: 0.7461 (mt)
REVERT: A  585 GLU cc_start: 0.7945 (pp20) cc_final: 0.7314 (pm20)
REVERT: A  628 ASP cc_start: 0.8325 (t0) cc_final: 0.7912 (t0)
REVERT: A  881 ARG cc_start: 0.6059 (tpm170) cc_final: 0.5665 (tpm170)
REVERT: B  318 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8238 (pt)
REVERT: B  437 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8607 (tt)
REVERT: B  472 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7656 (mm-30)
REVERT: B  501 PHE cc_start: 0.7934 (m-80) cc_final: 0.7552 (m-10)
  outliers start: 24
  outliers final: 17
  residues processed: 109
  average time/residue: 0.1736
  time to fit residues: 25.9845
Evaluate side-chains
  109 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 TRP
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  729 ASN
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0970
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0670
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 12 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 GLN
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.154136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.119476 restraints weight = 11295.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.119972 restraints weight = 7784.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.121231 restraints weight = 5374.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6576  Z= 0.171
  Angle     :  0.648   8.970   8882  Z= 0.314
  Chirality :  0.042   0.134    996
  Planarity :  0.004   0.041   1116
  Dihedral  :  4.195  19.356    854
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.72 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.63 (0.31), residues: 780
  helix:  0.76 (0.29), residues: 333
  sheet: -2.65 (0.64), residues: 66
  loop : -1.02 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 356 
 HIS   0.007   0.001   HIS B 509 
 PHE   0.016   0.001   PHE A 703 
 TYR   0.015   0.001   TYR A 460 
 ARG   0.009   0.000   ARG B 186 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 GLU cc_start: 0.7866 (tt0) cc_final: 0.7095 (pm20)
REVERT: A  486 GLN cc_start: 0.8195 (pm20) cc_final: 0.7933 (pm20)
REVERT: A  508 LEU cc_start: 0.8003 (tt) cc_final: 0.7475 (mt)
REVERT: A  585 GLU cc_start: 0.7888 (pp20) cc_final: 0.7349 (pm20)
REVERT: A  628 ASP cc_start: 0.8357 (t0) cc_final: 0.8015 (t0)
REVERT: A  713 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7884 (pm20)
REVERT: A  881 ARG cc_start: 0.6040 (tpm170) cc_final: 0.5639 (tpm170)
REVERT: B  232 GLU cc_start: 0.8271 (tp30) cc_final: 0.8065 (tp30)
REVERT: B  238 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8347 (mp10)
REVERT: B  318 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8297 (pt)
REVERT: B  472 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7833 (mm-30)
REVERT: B  501 PHE cc_start: 0.7974 (m-80) cc_final: 0.7586 (m-10)
  outliers start: 27
  outliers final: 21
  residues processed: 111
  average time/residue: 0.1728
  time to fit residues: 26.6439
Evaluate side-chains
  113 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  713 GLU
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  729 ASN
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  814 VAL
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  238 GLN
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  375 MET
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 32 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0170
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.154186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.120090 restraints weight = 11448.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.121505 restraints weight = 6413.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.122611 restraints weight = 5907.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6576  Z= 0.169
  Angle     :  0.656   9.051   8882  Z= 0.318
  Chirality :  0.043   0.148    996
  Planarity :  0.004   0.036   1116
  Dihedral  :  4.186  21.966    854
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 20.41 %
    Favored  : 75.86 %
  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: -0.59 (0.31), residues: 780
  helix:  0.80 (0.29), residues: 333
  sheet: -2.62 (0.64), residues: 66
  loop : -1.01 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 356 
 HIS   0.006   0.001   HIS B 335 
 PHE   0.016   0.001   PHE A 703 
 TYR   0.013   0.001   TYR B 383 
 ARG   0.008   0.000   ARG B 186 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 GLU cc_start: 0.7868 (tt0) cc_final: 0.7092 (pm20)
REVERT: A  486 GLN cc_start: 0.8194 (pm20) cc_final: 0.7913 (pm20)
REVERT: A  508 LEU cc_start: 0.8022 (tt) cc_final: 0.7494 (mt)
REVERT: A  585 GLU cc_start: 0.7869 (pp20) cc_final: 0.7334 (pm20)
REVERT: A  628 ASP cc_start: 0.8377 (t0) cc_final: 0.8033 (t0)
REVERT: A  713 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7879 (pm20)
REVERT: A  881 ARG cc_start: 0.5999 (tpm170) cc_final: 0.5590 (mmp-170)
REVERT: B  238 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8328 (mp10)
REVERT: B  318 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (pt)
REVERT: B  437 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8638 (tt)
REVERT: B  472 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7833 (mm-30)
REVERT: B  501 PHE cc_start: 0.7958 (m-80) cc_final: 0.7583 (m-10)
  outliers start: 27
  outliers final: 18
  residues processed: 109
  average time/residue: 0.1584
  time to fit residues: 24.4068
Evaluate side-chains
  111 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  713 GLU
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  814 VAL
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  238 GLN
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 804 ASN
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.149955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.116111 restraints weight = 11097.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.117239 restraints weight = 6968.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.118110 restraints weight = 6504.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6576  Z= 0.313
  Angle     :  0.723   9.684   8882  Z= 0.361
  Chirality :  0.046   0.148    996
  Planarity :  0.004   0.042   1116
  Dihedral  :  4.481  17.556    854
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 20.55 %
    Favored  : 75.86 %
  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: -0.88 (0.31), residues: 780
  helix:  0.54 (0.29), residues: 334
  sheet: -2.97 (0.64), residues: 68
  loop : -1.10 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 356 
 HIS   0.021   0.002   HIS B 509 
 PHE   0.022   0.002   PHE B 233 
 TYR   0.023   0.002   TYR A 799 
 ARG   0.005   0.001   ARG B 186 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 GLU cc_start: 0.7924 (tt0) cc_final: 0.7164 (pm20)
REVERT: A  508 LEU cc_start: 0.8076 (tt) cc_final: 0.7505 (mt)
REVERT: A  585 GLU cc_start: 0.7967 (pp20) cc_final: 0.7257 (pm20)
REVERT: A  881 ARG cc_start: 0.6340 (tpm170) cc_final: 0.5884 (mmp-170)
REVERT: B  238 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8487 (mp10)
REVERT: B  318 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8389 (pt)
REVERT: B  341 ASP cc_start: 0.7836 (m-30) cc_final: 0.7621 (m-30)
REVERT: B  472 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7849 (mm-30)
REVERT: B  501 PHE cc_start: 0.7958 (m-80) cc_final: 0.7563 (m-10)
  outliers start: 26
  outliers final: 20
  residues processed: 112
  average time/residue: 0.1489
  time to fit residues: 23.7666
Evaluate side-chains
  113 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  814 VAL
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  238 GLN
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  375 MET
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 75 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0040
   chunk 6 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.5794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 804 ASN
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.153965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.120790 restraints weight = 11098.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.122697 restraints weight = 6253.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.123550 restraints weight = 5005.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6576  Z= 0.176
  Angle     :  0.674  10.149   8882  Z= 0.329
  Chirality :  0.043   0.137    996
  Planarity :  0.004   0.040   1116
  Dihedral  :  4.268  17.102    854
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.10 %
    Favored  : 75.86 %
  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: -0.61 (0.31), residues: 780
  helix:  0.73 (0.29), residues: 334
  sheet: -2.49 (0.68), residues: 61
  loop : -1.03 (0.34), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 356 
 HIS   0.014   0.001   HIS B 509 
 PHE   0.022   0.001   PHE B 233 
 TYR   0.015   0.001   TYR B 383 
 ARG   0.006   0.000   ARG B 186 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2070.38 seconds
wall clock time: 37 minutes 54.74 seconds (2274.74 seconds total)