Starting phenix.real_space_refine
on Mon Jul 28 23:29:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1h_32941/07_2025/7x1h_32941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1h_32941/07_2025/7x1h_32941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x1h_32941/07_2025/7x1h_32941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1h_32941/07_2025/7x1h_32941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1h_32941/07_2025/7x1h_32941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1h_32941/07_2025/7x1h_32941.cif"
  }
  resolution = 2.96
  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=   0.024
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      60      5.16       5
     C    7084      2.51       5
     N    1770      2.21       5
     O    1846      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10760
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5380
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 28, 'TRANS': 647}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 5380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5380
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 28, 'TRANS': 647}
          Chain breaks: 6
  Time building chain proxies: 7.70, per 1000 atoms: 0.72
  Number of scatterers: 10760
  At special positions: 0
  Unit cell: (100.983, 105.909, 102.625, 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      60     16.00
     O    1846      8.00
     N    1770      7.00
     C    7084      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: 3.02
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2556

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 5 sheets defined
      66.9% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 147 through 160
      removed outlier: 3.700A  pdb=" N   PHE A 159 " --> pdb=" O   MET A 155 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 265 through 277
    Processing helix  chain 'A' and resid 278 through 288
      removed outlier: 3.603A  pdb=" N   GLN A 283 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 306
    Processing helix  chain 'A' and resid 343 through 354
    Processing helix  chain 'A' and resid 356 through 363
      removed outlier: 3.579A  pdb=" N   PHE A 361 " --> pdb=" O   TYR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 401
      Proline residue:  A 389  - end of helix
    Processing helix  chain 'A' and resid 406 through 424
    Processing helix  chain 'A' and resid 435 through 453
    Processing helix  chain 'A' and resid 455 through 477
    Processing helix  chain 'A' and resid 478 through 486
      removed outlier: 3.614A  pdb=" N   LEU A 481 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 518
      removed outlier: 3.501A  pdb=" N   GLU A 491 " --> pdb=" O   LYS A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 594
    Processing helix  chain 'A' and resid 595 through 597
      No H-bonds generated for 'chain 'A' and resid 595 through 597'
    Processing helix  chain 'A' and resid 601 through 611
      removed outlier: 3.710A  pdb=" N   SER A 609 " --> pdb=" O   ARG A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 626
      removed outlier: 3.531A  pdb=" N   ILE A 615 " --> pdb=" O   CYS A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 684
    Processing helix  chain 'A' and resid 685 through 689
    Processing helix  chain 'A' and resid 696 through 713
      removed outlier: 3.624A  pdb=" N   PHE A 713 " --> pdb=" O   GLY A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 732
      removed outlier: 3.820A  pdb=" N   LEU A 727 " --> pdb=" O   PRO A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 768
    Processing helix  chain 'A' and resid 769 through 772
    Processing helix  chain 'A' and resid 780 through 795
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 811 through 815
    Processing helix  chain 'A' and resid 819 through 824
    Processing helix  chain 'A' and resid 825 through 848
    Processing helix  chain 'A' and resid 851 through 856
    Processing helix  chain 'A' and resid 857 through 877
      removed outlier: 3.581A  pdb=" N   ILE A 861 " --> pdb=" O   ILE A 857 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ILE A 866 " --> pdb=" O   MET A 862 " (cutoff:3.500A)
      Proline residue:  A 867  - end of helix
      removed outlier: 4.297A  pdb=" N   LEU A 873 " --> pdb=" O   ARG A 869 " (cutoff:3.500A)
      Proline residue:  A 874  - end of helix
    Processing helix  chain 'A' and resid 878 through 887
    Processing helix  chain 'B' and resid 132 through 137
    Processing helix  chain 'B' and resid 147 through 160
      removed outlier: 3.652A  pdb=" N   PHE B 159 " --> pdb=" O   MET B 155 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'B' and resid 265 through 277
    Processing helix  chain 'B' and resid 278 through 288
      removed outlier: 3.604A  pdb=" N   GLN B 283 " --> pdb=" O   ILE B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 306
    Processing helix  chain 'B' and resid 343 through 354
    Processing helix  chain 'B' and resid 356 through 363
      removed outlier: 3.574A  pdb=" N   PHE B 361 " --> pdb=" O   TYR B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 401
      Proline residue:  B 389  - end of helix
    Processing helix  chain 'B' and resid 406 through 424
    Processing helix  chain 'B' and resid 435 through 453
    Processing helix  chain 'B' and resid 455 through 477
    Processing helix  chain 'B' and resid 478 through 486
      removed outlier: 3.611A  pdb=" N   LEU B 481 " --> pdb=" O   ASN B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 518
    Processing helix  chain 'B' and resid 570 through 594
    Processing helix  chain 'B' and resid 595 through 597
      No H-bonds generated for 'chain 'B' and resid 595 through 597'
    Processing helix  chain 'B' and resid 601 through 611
    Processing helix  chain 'B' and resid 612 through 626
    Processing helix  chain 'B' and resid 654 through 684
    Processing helix  chain 'B' and resid 685 through 689
    Processing helix  chain 'B' and resid 696 through 713
      removed outlier: 3.624A  pdb=" N   PHE B 713 " --> pdb=" O   GLY B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 723 through 732
      removed outlier: 3.826A  pdb=" N   LEU B 727 " --> pdb=" O   PRO B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 755 through 768
    Processing helix  chain 'B' and resid 769 through 772
    Processing helix  chain 'B' and resid 780 through 795
    Processing helix  chain 'B' and resid 799 through 807
    Processing helix  chain 'B' and resid 811 through 815
    Processing helix  chain 'B' and resid 819 through 824
    Processing helix  chain 'B' and resid 825 through 848
    Processing helix  chain 'B' and resid 851 through 856
    Processing helix  chain 'B' and resid 857 through 877
      removed outlier: 3.572A  pdb=" N   ILE B 861 " --> pdb=" O   ILE B 857 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ILE B 866 " --> pdb=" O   MET B 862 " (cutoff:3.500A)
      Proline residue:  B 867  - end of helix
      removed outlier: 4.309A  pdb=" N   LEU B 873 " --> pdb=" O   ARG B 869 " (cutoff:3.500A)
      Proline residue:  B 874  - end of helix
    Processing helix  chain 'B' and resid 878 through 887
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 143
      removed outlier: 5.469A  pdb=" N   VAL A 235 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ARG A 248 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 13.208A  pdb=" N   VAL A 247 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 11.909A  pdb=" N   GLN A 211 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   PHE A 249 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   SER A 213 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   ILE A 251 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LEU A 215 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   VAL A 253 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ILE A 217 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   ALA A 255 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   CYS A 219 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   GLY A 200 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 9.074A  pdb=" N   SER A 213 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 11.851A  pdb=" N   ILE A 198 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      removed outlier: 9.752A  pdb=" N   LEU A 215 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
      removed outlier: 10.947A  pdb=" N   ASP A 196 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU B 107 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU A 107 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 10.837A  pdb=" N   ASP B 196 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 9.641A  pdb=" N   LEU B 215 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 11.863A  pdb=" N   ILE B 198 " --> pdb=" O   SER B 213 " (cutoff:3.500A)
      removed outlier: 9.152A  pdb=" N   SER B 213 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLY B 200 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      removed outlier: 13.199A  pdb=" N   VAL B 247 " --> pdb=" O   ARG B 209 " (cutoff:3.500A)
      removed outlier: 12.011A  pdb=" N   GLN B 211 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 8.713A  pdb=" N   PHE B 249 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   SER B 213 " --> pdb=" O   PHE B 249 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   ILE B 251 " --> pdb=" O   SER B 213 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LEU B 215 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   VAL B 253 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE B 217 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ALA B 255 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   CYS B 219 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   VAL B 235 " --> pdb=" O   ASN B 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 432 through 433
    Processing sheet with id=AA3, first strand: chain 'A' and resid 733 through 740
      removed outlier: 6.742A  pdb=" N   LEU A 734 " --> pdb=" O   VAL A 749 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 432 through 433
    Processing sheet with id=AA5, first strand: chain 'B' and resid 733 through 740
      removed outlier: 6.745A  pdb=" N   LEU B 734 " --> pdb=" O   VAL B 749 " (cutoff:3.500A)

    688 hydrogen bonds defined for protein.
    1962 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: 3.48

  Time building geometry restraints manager: 3.53 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2309
        1.33 -     1.45: 2352
        1.45 -     1.57: 6245
        1.57 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 11004
  Sorted by residual:
  bond pdb=" CA  GLN A 238 "
       pdb=" C   GLN A 238 "
    ideal  model  delta    sigma   weight residual
    1.522  1.473  0.050 1.20e-02 6.94e+03 1.72e+01
  bond pdb=" C   ILE B 251 "
       pdb=" O   ILE B 251 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.026 1.08e-02 8.57e+03 5.74e+00
  bond pdb=" C   ASP B 360 "
       pdb=" O   ASP B 360 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.17e-02 7.31e+03 4.54e+00
  bond pdb=" C   ASP A 360 "
       pdb=" O   ASP A 360 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.17e-02 7.31e+03 4.42e+00
  bond pdb=" C   PRO A 816 "
       pdb=" O   PRO A 816 "
    ideal  model  delta    sigma   weight residual
    1.240  1.217  0.023 1.12e-02 7.97e+03 4.25e+00
  ... (remaining 10999 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 14646
        1.70 -     3.40: 225
        3.40 -     5.10: 48
        5.10 -     6.80: 13
        6.80 -     8.50: 2
  Bond angle restraints: 14934
  Sorted by residual:
  angle pdb=" N   CYS B 245 "
        pdb=" CA  CYS B 245 "
        pdb=" C   CYS B 245 "
      ideal   model   delta    sigma   weight residual
     112.54  119.16   -6.62 1.22e+00 6.72e-01 2.94e+01
  angle pdb=" N   THR A 362 "
        pdb=" CA  THR A 362 "
        pdb=" C   THR A 362 "
      ideal   model   delta    sigma   weight residual
     112.59  118.28   -5.69 1.22e+00 6.72e-01 2.18e+01
  angle pdb=" N   THR B 362 "
        pdb=" CA  THR B 362 "
        pdb=" C   THR B 362 "
      ideal   model   delta    sigma   weight residual
     112.26  118.22   -5.96 1.32e+00 5.74e-01 2.04e+01
  angle pdb=" N   VAL B 247 "
        pdb=" CA  VAL B 247 "
        pdb=" C   VAL B 247 "
      ideal   model   delta    sigma   weight residual
     109.34  117.45   -8.11 2.08e+00 2.31e-01 1.52e+01
  angle pdb=" N   ASP B 360 "
        pdb=" CA  ASP B 360 "
        pdb=" C   ASP B 360 "
      ideal   model   delta    sigma   weight residual
     111.28  107.19    4.09 1.09e+00 8.42e-01 1.41e+01
  ... (remaining 14929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.27: 5805
       16.27 -    32.53: 587
       32.53 -    48.80: 110
       48.80 -    65.07: 16
       65.07 -    81.33: 8
  Dihedral angle restraints: 6526
    sinusoidal: 2574
      harmonic: 3952
  Sorted by residual:
  dihedral pdb=" C   PHE A 361 "
           pdb=" N   PHE A 361 "
           pdb=" CA  PHE A 361 "
           pdb=" CB  PHE A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.92    8.32     0      2.50e+00 1.60e-01 1.11e+01
  dihedral pdb=" C   PHE B 361 "
           pdb=" N   PHE B 361 "
           pdb=" CA  PHE B 361 "
           pdb=" CB  PHE B 361 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.79    8.19     0      2.50e+00 1.60e-01 1.07e+01
  dihedral pdb=" CB  LYS B 512 "
           pdb=" CG  LYS B 512 "
           pdb=" CD  LYS B 512 "
           pdb=" CE  LYS B 512 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.60   59.60     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 6523 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1564
       0.065 -    0.129: 179
       0.129 -    0.194: 15
       0.194 -    0.259: 2
       0.259 -    0.323: 4
  Chirality restraints: 1764
  Sorted by residual:
  chirality pdb=" CA  PHE A 361 "
            pdb=" N   PHE A 361 "
            pdb=" C   PHE A 361 "
            pdb=" CB  PHE A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CA  PHE B 361 "
            pdb=" N   PHE B 361 "
            pdb=" C   PHE B 361 "
            pdb=" CB  PHE B 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  PHE A 354 "
            pdb=" N   PHE A 354 "
            pdb=" C   PHE A 354 "
            pdb=" CB  PHE A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1761 not shown)

  Planarity restraints: 1828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 213 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.23e+00
        pdb=" C   SER B 213 "    0.047 2.00e-02 2.50e+03
        pdb=" O   SER B 213 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TRP B 214 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 774 "    0.038 5.00e-02 4.00e+02   5.78e-02 5.34e+00
        pdb=" N   PRO B 775 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 775 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 775 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 774 "   -0.038 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO A 775 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 775 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 775 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1825 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1409
        2.75 -     3.29: 10665
        3.29 -     3.83: 18273
        3.83 -     4.36: 21592
        4.36 -     4.90: 38037
  Nonbonded interactions: 89976
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 386 "
            pdb=" OG1 THR B 390 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   CYS A 386 "
            pdb=" OG1 THR A 390 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   LEU A 600 "
            pdb=" NH1 ARG A 605 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NE2 GLN B 414 "
            pdb=" O   LEU B 432 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" NE2 GLN A 414 "
            pdb=" O   LEU A 432 "
     model   vdw
     2.271 3.120
  ... (remaining 89971 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             34.540
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.560
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.050
  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:15.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   80.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
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      :  0.003   0.050  11004  Z= 0.177
  Angle     :  0.564   8.498  14934  Z= 0.328
  Chirality :  0.042   0.323   1764
  Planarity :  0.004   0.058   1828
  Dihedral  : 13.096  81.334   3970
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.26 %
    Favored  : 99.57 %
  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:  2.35 (0.24), residues: 1324
  helix:  2.33 (0.18), residues: 848
  sheet:  0.18 (0.42), residues: 108
  loop :  0.20 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 515 
 HIS   0.003   0.001   HIS B 192 
 PHE   0.019   0.001   PHE A 846 
 TYR   0.014   0.001   TYR B 357 
 ARG   0.007   0.000   ARG A 822 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12385 (  688)
  hydrogen bonds       : angle       4.62633 ( 1962)
  covalent geometry    : bond        0.00285 (11004)
  covalent geometry    : angle       0.56449 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 268
  time to evaluate  : 1.320 
Fit side-chains
REVERT: A  175 LEU cc_start: 0.7450 (mp) cc_final: 0.7189 (tt)
REVERT: A  267 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6478 (pt0)
REVERT: A  354 PHE cc_start: 0.8632 (t80) cc_final: 0.8406 (t80)
REVERT: A  477 PHE cc_start: 0.8225 (m-80) cc_final: 0.7900 (m-10)
REVERT: B  175 LEU cc_start: 0.7469 (mp) cc_final: 0.7175 (tt)
REVERT: B  354 PHE cc_start: 0.8657 (t80) cc_final: 0.8415 (t80)
REVERT: B  477 PHE cc_start: 0.8222 (m-80) cc_final: 0.7949 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 270
  average time/residue: 1.4876
  time to fit residues: 435.8551
Evaluate side-chains
  163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  868 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 243 ASN
A 800 GLN
B 478 ASN
B 649 GLN
B 800 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.123967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.099144 restraints weight = 12961.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.89
r_work: 0.2880 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.080  11004  Z= 0.380
  Angle     :  0.791  11.519  14934  Z= 0.394
  Chirality :  0.051   0.194   1764
  Planarity :  0.006   0.047   1828
  Dihedral  :  4.582  21.000   1464
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 11.99 %
    Favored  : 84.50 %
  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:  1.04 (0.22), residues: 1324
  helix:  1.42 (0.17), residues: 846
  sheet: -0.28 (0.41), residues: 114
  loop : -0.60 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 778 
 HIS   0.012   0.002   HIS B 719 
 PHE   0.023   0.003   PHE B 620 
 TYR   0.017   0.002   TYR A 638 
 ARG   0.008   0.001   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05811 (  688)
  hydrogen bonds       : angle       4.57553 ( 1962)
  covalent geometry    : bond        0.00945 (11004)
  covalent geometry    : angle       0.79118 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 161
  time to evaluate  : 1.368 
Fit side-chains
REVERT: A  116 LYS cc_start: 0.8375 (mtmt) cc_final: 0.8085 (ptmt)
REVERT: A  221 MET cc_start: 0.5933 (mtp) cc_final: 0.5585 (mtt)
REVERT: A  354 PHE cc_start: 0.8562 (t80) cc_final: 0.8278 (t80)
REVERT: A  441 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8365 (m-80)
REVERT: A  854 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8388 (ttm)
REVERT: A  878 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6397 (mp0)
REVERT: A  881 TYR cc_start: 0.7555 (m-10) cc_final: 0.7064 (m-80)
REVERT: B  116 LYS cc_start: 0.8314 (mtmt) cc_final: 0.8040 (ptmt)
REVERT: B  221 MET cc_start: 0.5850 (mtp) cc_final: 0.5558 (mtt)
REVERT: B  354 PHE cc_start: 0.8575 (t80) cc_final: 0.8294 (t80)
REVERT: B  441 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8379 (m-80)
REVERT: B  477 PHE cc_start: 0.8215 (m-80) cc_final: 0.7804 (m-10)
REVERT: B  878 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6457 (mp0)
REVERT: B  881 TYR cc_start: 0.7503 (m-10) cc_final: 0.7039 (m-80)
  outliers start: 41
  outliers final: 10
  residues processed: 196
  average time/residue: 1.2312
  time to fit residues: 263.1486
Evaluate side-chains
  147 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  441 TYR
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  854 MET
Chi-restraints excluded: chain A residue  878 GLU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  878 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 98 optimal weight:    0.5980
   chunk 72 optimal weight:    0.3980
   chunk 43 optimal weight:    0.7980
   chunk 115 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.128272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.103265 restraints weight = 12873.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.94
r_work: 0.2897 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11004  Z= 0.138
  Angle     :  0.519   6.377  14934  Z= 0.267
  Chirality :  0.039   0.154   1764
  Planarity :  0.004   0.039   1828
  Dihedral  :  4.078  18.111   1462
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 13.36 %
    Favored  : 82.02 %
  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:  1.47 (0.23), residues: 1324
  helix:  1.72 (0.18), residues: 836
  sheet:  0.13 (0.42), residues: 112
  loop : -0.35 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 515 
 HIS   0.004   0.001   HIS B 192 
 PHE   0.021   0.001   PHE B 620 
 TYR   0.013   0.001   TYR B 441 
 ARG   0.003   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  688)
  hydrogen bonds       : angle       4.16852 ( 1962)
  covalent geometry    : bond        0.00326 (11004)
  covalent geometry    : angle       0.51906 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 158
  time to evaluate  : 1.708 
Fit side-chains
REVERT: A  116 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7693 (mmtt)
REVERT: A  154 THR cc_start: 0.8270 (m) cc_final: 0.7737 (p)
REVERT: A  221 MET cc_start: 0.5760 (mtp) cc_final: 0.5466 (mtt)
REVERT: A  278 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7118 (t70)
REVERT: A  289 ARG cc_start: 0.7629 (mmt180) cc_final: 0.7296 (mmt-90)
REVERT: A  354 PHE cc_start: 0.8512 (t80) cc_final: 0.8257 (t80)
REVERT: A  647 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7790 (ttt)
REVERT: A  662 MET cc_start: 0.8423 (ttm) cc_final: 0.8005 (ttm)
REVERT: A  687 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7817 (pm20)
REVERT: A  881 TYR cc_start: 0.7434 (m-10) cc_final: 0.7002 (m-80)
REVERT: B  116 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7708 (mmtt)
REVERT: B  154 THR cc_start: 0.8254 (m) cc_final: 0.7709 (p)
REVERT: B  221 MET cc_start: 0.5801 (mtp) cc_final: 0.5579 (mtt)
REVERT: B  278 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7098 (t70)
REVERT: B  289 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7301 (mmt-90)
REVERT: B  354 PHE cc_start: 0.8527 (t80) cc_final: 0.8272 (t80)
REVERT: B  477 PHE cc_start: 0.8187 (m-80) cc_final: 0.7900 (m-10)
REVERT: B  647 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7758 (ttt)
REVERT: B  656 ARG cc_start: 0.5932 (ttp80) cc_final: 0.5732 (ttp-110)
REVERT: B  662 MET cc_start: 0.8433 (ttm) cc_final: 0.8035 (ttm)
REVERT: B  881 TYR cc_start: 0.7456 (m-10) cc_final: 0.7116 (m-80)
  outliers start: 54
  outliers final: 18
  residues processed: 196
  average time/residue: 1.4803
  time to fit residues: 315.8143
Evaluate side-chains
  157 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 1.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  370 LYS
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  278 ASP
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  647 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 115 optimal weight:    3.9990
   chunk 119 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 228 HIS
B 142 ASN
B 228 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.116437 restraints weight = 12197.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.61
r_work: 0.3202 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11004  Z= 0.157
  Angle     :  0.521   6.360  14934  Z= 0.266
  Chirality :  0.040   0.157   1764
  Planarity :  0.004   0.038   1828
  Dihedral  :  4.021  17.727   1462
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 15.15 %
    Favored  : 80.57 %
  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:  1.51 (0.23), residues: 1324
  helix:  1.75 (0.18), residues: 836
  sheet:  0.12 (0.41), residues: 114
  loop : -0.35 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 515 
 HIS   0.005   0.001   HIS A 719 
 PHE   0.019   0.001   PHE A 620 
 TYR   0.013   0.001   TYR A 441 
 ARG   0.003   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  688)
  hydrogen bonds       : angle       4.14396 ( 1962)
  covalent geometry    : bond        0.00383 (11004)
  covalent geometry    : angle       0.52121 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 141
  time to evaluate  : 1.153 
Fit side-chains
REVERT: A  116 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7879 (mmtt)
REVERT: A  154 THR cc_start: 0.8516 (m) cc_final: 0.8006 (p)
REVERT: A  278 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7417 (t70)
REVERT: A  354 PHE cc_start: 0.8689 (t80) cc_final: 0.8427 (t80)
REVERT: A  662 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8210 (ttm)
REVERT: A  687 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7962 (pm20)
REVERT: A  793 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8755 (mp)
REVERT: A  881 TYR cc_start: 0.7617 (m-10) cc_final: 0.7246 (m-80)
REVERT: B  116 LYS cc_start: 0.8468 (mtmt) cc_final: 0.7885 (mmtt)
REVERT: B  154 THR cc_start: 0.8506 (m) cc_final: 0.8007 (p)
REVERT: B  278 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7391 (t70)
REVERT: B  354 PHE cc_start: 0.8705 (t80) cc_final: 0.8450 (t80)
REVERT: B  662 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8235 (ttm)
REVERT: B  793 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8762 (mp)
REVERT: B  881 TYR cc_start: 0.7642 (m-10) cc_final: 0.7364 (m-80)
  outliers start: 50
  outliers final: 23
  residues processed: 170
  average time/residue: 1.1517
  time to fit residues: 215.1626
Evaluate side-chains
  159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  370 LYS
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  278 ASP
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 87 optimal weight:    0.0370
   chunk 110 optimal weight:    0.4980
   chunk 52 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 95 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
B 142 ASN
B 283 GLN
B 649 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.140789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.118192 restraints weight = 12124.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.64
r_work: 0.3218 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11004  Z= 0.127
  Angle     :  0.489   6.434  14934  Z= 0.251
  Chirality :  0.039   0.152   1764
  Planarity :  0.004   0.039   1828
  Dihedral  :  3.892  16.665   1462
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 15.92 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.63 (0.23), residues: 1324
  helix:  1.84 (0.18), residues: 834
  sheet:  0.23 (0.42), residues: 114
  loop : -0.29 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 515 
 HIS   0.004   0.001   HIS B 719 
 PHE   0.019   0.001   PHE B 620 
 TYR   0.010   0.001   TYR B 441 
 ARG   0.003   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04057 (  688)
  hydrogen bonds       : angle       4.07602 ( 1962)
  covalent geometry    : bond        0.00298 (11004)
  covalent geometry    : angle       0.48858 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 140
  time to evaluate  : 1.334 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7983 (m) cc_final: 0.7733 (p)
REVERT: A  116 LYS cc_start: 0.8531 (mtmt) cc_final: 0.7882 (mmtt)
REVERT: A  154 THR cc_start: 0.8449 (m) cc_final: 0.7993 (p)
REVERT: A  354 PHE cc_start: 0.8733 (t80) cc_final: 0.8473 (t80)
REVERT: A  633 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8400 (ptm)
REVERT: A  662 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8203 (ttm)
REVERT: A  687 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7972 (pm20)
REVERT: A  793 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8751 (mp)
REVERT: A  881 TYR cc_start: 0.7652 (m-10) cc_final: 0.7255 (m-80)
REVERT: B  106 VAL cc_start: 0.8052 (m) cc_final: 0.7790 (p)
REVERT: B  116 LYS cc_start: 0.8496 (mtmt) cc_final: 0.7869 (mmtt)
REVERT: B  354 PHE cc_start: 0.8729 (t80) cc_final: 0.8466 (t80)
REVERT: B  662 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8213 (ttm)
REVERT: B  687 GLU cc_start: 0.8172 (pt0) cc_final: 0.7962 (pm20)
REVERT: B  793 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8759 (mp)
REVERT: B  881 TYR cc_start: 0.7652 (m-10) cc_final: 0.7345 (m-80)
  outliers start: 44
  outliers final: 22
  residues processed: 165
  average time/residue: 1.0042
  time to fit residues: 182.9564
Evaluate side-chains
  163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
A 800 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.137634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.115091 restraints weight = 12260.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.63
r_work: 0.3172 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11004  Z= 0.158
  Angle     :  0.531   9.066  14934  Z= 0.266
  Chirality :  0.040   0.161   1764
  Planarity :  0.004   0.040   1828
  Dihedral  :  3.951  17.253   1462
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.01 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.51 (0.23), residues: 1324
  helix:  1.73 (0.18), residues: 842
  sheet:  0.21 (0.43), residues: 114
  loop : -0.35 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 515 
 HIS   0.006   0.001   HIS B 719 
 PHE   0.018   0.001   PHE B 620 
 TYR   0.011   0.001   TYR B 722 
 ARG   0.003   0.000   ARG A 637 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04307 (  688)
  hydrogen bonds       : angle       4.13048 ( 1962)
  covalent geometry    : bond        0.00386 (11004)
  covalent geometry    : angle       0.53142 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 137
  time to evaluate  : 1.222 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7954 (m) cc_final: 0.7702 (p)
REVERT: A  116 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7781 (mmtt)
REVERT: A  154 THR cc_start: 0.8410 (m) cc_final: 0.7921 (p)
REVERT: A  278 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7295 (t70)
REVERT: A  354 PHE cc_start: 0.8699 (t80) cc_final: 0.8433 (t80)
REVERT: A  633 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8365 (ptm)
REVERT: A  647 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7850 (ttt)
REVERT: A  662 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8168 (ttm)
REVERT: A  687 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7919 (pm20)
REVERT: A  793 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8703 (mp)
REVERT: A  881 TYR cc_start: 0.7586 (m-10) cc_final: 0.7218 (m-80)
REVERT: B  106 VAL cc_start: 0.7966 (m) cc_final: 0.7696 (p)
REVERT: B  116 LYS cc_start: 0.8483 (mtmt) cc_final: 0.7795 (mmtt)
REVERT: B  278 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7266 (t70)
REVERT: B  354 PHE cc_start: 0.8712 (t80) cc_final: 0.8440 (t80)
REVERT: B  647 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7841 (ttt)
REVERT: B  662 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8187 (ttm)
REVERT: B  793 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8717 (mp)
REVERT: B  881 TYR cc_start: 0.7594 (m-10) cc_final: 0.7334 (m-80)
  outliers start: 43
  outliers final: 23
  residues processed: 162
  average time/residue: 1.1044
  time to fit residues: 198.0869
Evaluate side-chains
  163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  278 ASP
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  647 MET
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 131 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 130 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN
A 800 GLN
B 639 ASN
B 649 GLN
B 800 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.137160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.114653 restraints weight = 12417.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.63
r_work: 0.3173 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11004  Z= 0.161
  Angle     :  0.537   8.973  14934  Z= 0.267
  Chirality :  0.040   0.161   1764
  Planarity :  0.004   0.040   1828
  Dihedral  :  3.962  17.224   1462
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.10 %
    Favored  : 80.14 %
  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:  1.51 (0.23), residues: 1324
  helix:  1.71 (0.18), residues: 842
  sheet:  0.30 (0.44), residues: 114
  loop : -0.34 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 515 
 HIS   0.005   0.001   HIS B 719 
 PHE   0.018   0.001   PHE B 620 
 TYR   0.011   0.001   TYR A 441 
 ARG   0.006   0.000   ARG B 637 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  688)
  hydrogen bonds       : angle       4.15445 ( 1962)
  covalent geometry    : bond        0.00393 (11004)
  covalent geometry    : angle       0.53669 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 134
  time to evaluate  : 1.881 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7807 (m) cc_final: 0.7548 (p)
REVERT: A  116 LYS cc_start: 0.8428 (mtmt) cc_final: 0.7602 (mmtt)
REVERT: A  278 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7024 (t70)
REVERT: A  354 PHE cc_start: 0.8595 (t80) cc_final: 0.8326 (t80)
REVERT: A  633 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8207 (ptm)
REVERT: A  647 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7850 (ttt)
REVERT: A  662 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8042 (ttm)
REVERT: A  687 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7732 (pm20)
REVERT: A  793 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8494 (mp)
REVERT: B  106 VAL cc_start: 0.7862 (m) cc_final: 0.7605 (p)
REVERT: B  116 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7619 (mmtt)
REVERT: B  278 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7023 (t70)
REVERT: B  287 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7094 (mm-30)
REVERT: B  354 PHE cc_start: 0.8596 (t80) cc_final: 0.8314 (t80)
REVERT: B  647 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7832 (ttt)
REVERT: B  662 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8045 (ttm)
REVERT: B  793 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8508 (mp)
REVERT: B  881 TYR cc_start: 0.7419 (m-10) cc_final: 0.7108 (m-80)
  outliers start: 44
  outliers final: 24
  residues processed: 160
  average time/residue: 1.3411
  time to fit residues: 235.6718
Evaluate side-chains
  163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 1.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  278 ASP
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  647 MET
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 133 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN
B 639 ASN
B 649 GLN
B 800 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.136768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.114442 restraints weight = 12206.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.62
r_work: 0.3171 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11004  Z= 0.162
  Angle     :  0.545   9.280  14934  Z= 0.269
  Chirality :  0.040   0.164   1764
  Planarity :  0.004   0.039   1828
  Dihedral  :  3.968  17.347   1462
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.27 %
    Favored  : 80.05 %
  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:  1.52 (0.23), residues: 1324
  helix:  1.72 (0.18), residues: 844
  sheet:  0.26 (0.45), residues: 112
  loop : -0.33 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 515 
 HIS   0.005   0.001   HIS B 719 
 PHE   0.018   0.001   PHE A 620 
 TYR   0.011   0.001   TYR A 441 
 ARG   0.006   0.000   ARG A 637 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04323 (  688)
  hydrogen bonds       : angle       4.14518 ( 1962)
  covalent geometry    : bond        0.00397 (11004)
  covalent geometry    : angle       0.54507 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 137
  time to evaluate  : 2.694 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7866 (m) cc_final: 0.7621 (p)
REVERT: A  116 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7535 (mmtt)
REVERT: A  278 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7000 (t70)
REVERT: A  287 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7149 (mm-30)
REVERT: A  354 PHE cc_start: 0.8596 (t80) cc_final: 0.8329 (t80)
REVERT: A  662 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8013 (ttm)
REVERT: A  687 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7713 (pm20)
REVERT: A  793 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8478 (mp)
REVERT: B  106 VAL cc_start: 0.7860 (m) cc_final: 0.7594 (p)
REVERT: B  116 LYS cc_start: 0.8432 (mtmt) cc_final: 0.7722 (ttpt)
REVERT: B  278 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6996 (t70)
REVERT: B  354 PHE cc_start: 0.8590 (t80) cc_final: 0.8316 (t80)
REVERT: B  441 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8377 (m-80)
REVERT: B  633 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7552 (mtp)
REVERT: B  647 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7849 (ttt)
REVERT: B  662 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8052 (ttm)
REVERT: B  793 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8499 (mp)
REVERT: B  881 TYR cc_start: 0.7423 (m-10) cc_final: 0.7111 (m-80)
  outliers start: 43
  outliers final: 26
  residues processed: 162
  average time/residue: 1.1209
  time to fit residues: 202.7175
Evaluate side-chains
  167 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  278 ASP
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  647 MET
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  876 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 122 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 110 optimal weight:    0.4980
   chunk 128 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0070
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN
B 639 ASN
B 649 GLN
B 800 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.138428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.116211 restraints weight = 12297.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.63
r_work: 0.3219 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11004  Z= 0.125
  Angle     :  0.519   9.699  14934  Z= 0.257
  Chirality :  0.039   0.155   1764
  Planarity :  0.004   0.040   1828
  Dihedral  :  3.875  16.365   1462
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 16.87 %
    Favored  : 79.88 %
  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:  1.63 (0.23), residues: 1324
  helix:  1.79 (0.18), residues: 844
  sheet:  0.44 (0.47), residues: 112
  loop : -0.30 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 515 
 HIS   0.004   0.001   HIS B 719 
 PHE   0.017   0.001   PHE B 620 
 TYR   0.011   0.001   TYR A 441 
 ARG   0.005   0.000   ARG A 637 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04029 (  688)
  hydrogen bonds       : angle       4.10466 ( 1962)
  covalent geometry    : bond        0.00296 (11004)
  covalent geometry    : angle       0.51923 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 1.641 
Fit side-chains
REVERT: A  116 LYS cc_start: 0.8447 (mtmt) cc_final: 0.7732 (mmtt)
REVERT: A  354 PHE cc_start: 0.8665 (t80) cc_final: 0.8437 (t80)
REVERT: A  662 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8173 (ttm)
REVERT: A  687 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7892 (pm20)
REVERT: A  793 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8723 (mp)
REVERT: B  106 VAL cc_start: 0.7997 (m) cc_final: 0.7784 (p)
REVERT: B  116 LYS cc_start: 0.8469 (mtmt) cc_final: 0.7879 (ttpt)
REVERT: B  178 MET cc_start: 0.8013 (mtp) cc_final: 0.7771 (mtt)
REVERT: B  278 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7178 (t70)
REVERT: B  354 PHE cc_start: 0.8683 (t80) cc_final: 0.8438 (t80)
REVERT: B  633 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7689 (mtm)
REVERT: B  662 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8181 (ttm)
REVERT: B  793 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8726 (mp)
REVERT: B  881 TYR cc_start: 0.7573 (m-10) cc_final: 0.7223 (m-80)
  outliers start: 38
  outliers final: 22
  residues processed: 160
  average time/residue: 1.2038
  time to fit residues: 213.9360
Evaluate side-chains
  162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  278 ASP
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  876 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 125 optimal weight:    0.7980
   chunk 93 optimal weight:    0.4980
   chunk 21 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0870
   chunk 1 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.0762

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN
A 800 GLN
B 639 ASN
B 649 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.135912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113526 restraints weight = 12226.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.62
r_work: 0.3157 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11004  Z= 0.187
  Angle     :  0.578   9.504  14934  Z= 0.287
  Chirality :  0.041   0.172   1764
  Planarity :  0.004   0.037   1828
  Dihedral  :  4.034  17.831   1462
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.98 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.40 (0.23), residues: 1324
  helix:  1.64 (0.18), residues: 842
  sheet:  0.27 (0.45), residues: 112
  loop : -0.43 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 515 
 HIS   0.006   0.001   HIS B 719 
 PHE   0.020   0.002   PHE B 858 
 TYR   0.011   0.001   TYR A 441 
 ARG   0.006   0.000   ARG A 637 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04497 (  688)
  hydrogen bonds       : angle       4.23646 ( 1962)
  covalent geometry    : bond        0.00462 (11004)
  covalent geometry    : angle       0.57832 (14934)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 1.841 
Fit side-chains
REVERT: A  116 LYS cc_start: 0.8469 (mtmt) cc_final: 0.7647 (mmpt)
REVERT: A  292 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7124 (mp0)
REVERT: A  354 PHE cc_start: 0.8596 (t80) cc_final: 0.8327 (t80)
REVERT: A  662 MET cc_start: 0.8485 (ttm) cc_final: 0.8083 (ttm)
REVERT: A  687 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7711 (pm20)
REVERT: A  793 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8481 (mp)
REVERT: B  106 VAL cc_start: 0.7853 (m) cc_final: 0.7604 (p)
REVERT: B  116 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7769 (ttpt)
REVERT: B  278 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7017 (t70)
REVERT: B  292 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7121 (mp0)
REVERT: B  354 PHE cc_start: 0.8590 (t80) cc_final: 0.8323 (t80)
REVERT: B  633 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7726 (mtm)
REVERT: B  662 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8082 (ttm)
REVERT: B  793 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8473 (mp)
REVERT: B  881 TYR cc_start: 0.7411 (m-10) cc_final: 0.7076 (m-80)
  outliers start: 31
  outliers final: 22
  residues processed: 158
  average time/residue: 1.1474
  time to fit residues: 200.3415
Evaluate side-chains
  162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  278 ASP
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  633 MET
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  848 MET
Chi-restraints excluded: chain B residue  876 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   chunk 98 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 112 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN
A 741 ASN
B 639 ASN
B 649 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.137410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.115129 restraints weight = 12214.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.62
r_work: 0.3184 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11004  Z= 0.142
  Angle     :  0.541   9.784  14934  Z= 0.268
  Chirality :  0.039   0.158   1764
  Planarity :  0.004   0.038   1828
  Dihedral  :  3.953  16.861   1462
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.72 %
    Favored  : 79.45 %
  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:  1.53 (0.23), residues: 1324
  helix:  1.71 (0.18), residues: 842
  sheet:  0.46 (0.47), residues: 110
  loop : -0.34 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 515 
 HIS   0.004   0.001   HIS B 719 
 PHE   0.017   0.001   PHE B 620 
 TYR   0.011   0.001   TYR A 441 
 ARG   0.005   0.000   ARG A 637 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04186 (  688)
  hydrogen bonds       : angle       4.15689 ( 1962)
  covalent geometry    : bond        0.00340 (11004)
  covalent geometry    : angle       0.54078 (14934)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9069.46 seconds
wall clock time: 166 minutes 16.60 seconds (9976.60 seconds total)