Starting phenix.real_space_refine
on Tue Jan 14 00:31:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.cif"
  }
  resolution = 3.59
  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=  -0.002 sd=   0.093
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: 5
    Type Number    sf(0)   Gaussians
     Zn      8      6.06       5
     S      41      5.16       5
     C    3071      2.51       5
     N     829      2.21       5
     O     805      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 4754
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2362
          Classifications: {'peptide': 315}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 11, 'TRANS': 303}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 56
    Chain: "B"
      Number of atoms: 2384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2384
          Classifications: {'peptide': 315}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 11, 'TRANS': 303}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 50
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 3.43, per 1000 atoms: 0.72
  Number of scatterers: 4754
  At special positions: 0
  Unit cell: (70.655, 58.698, 117.396, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      8     29.99
     S      41     16.00
     O     805      8.00
     N     829      7.00
     C    3071      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 286 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS B 291 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 286 " - pdb=" SG  CYS B 311 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 674.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS B 157 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 370 "
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" NE2 HIS A  43 "
        pdb="ZN    ZN A 602 " - pdb=" NE2 HIS A 251 "
      pdb="  ZN A 603 "
        pdb="ZN    ZN A 603 " - pdb=" NE2 HIS A 373 "
        pdb="ZN    ZN A 603 " - pdb=" NE2 HIS B 148 "
        pdb="ZN    ZN A 603 " - pdb=" NE2 HIS B 146 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" NE2 HIS A 157 "
        pdb="ZN    ZN B 601 " - pdb=" NE2 HIS B 370 "
      pdb="  ZN B 602 "
        pdb="ZN    ZN B 602 " - pdb=" NE2 HIS B  43 "
        pdb="ZN    ZN B 602 " - pdb=" NE2 HIS B 251 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS B 373 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS A 148 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS A 146 "


  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      68.1% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 33
    Processing helix  chain 'A' and resid 35 through 62
      removed outlier: 3.514A  pdb=" N   LEU A  45 " --> pdb=" O   SER A  41 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ALA A  57 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ARG A  62 " --> pdb=" O   GLU A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 106
      removed outlier: 3.532A  pdb=" N   GLU A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 134
    Processing helix  chain 'A' and resid 239 through 273
    Processing helix  chain 'A' and resid 310 through 315
      removed outlier: 4.239A  pdb=" N   LEU A 314 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR A 315 " --> pdb=" O   CYS A 311 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 310 through 315'
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.622A  pdb=" N   THR A 319 " --> pdb=" O   TYR A 315 " (cutoff:3.500A)
      Proline residue:  A 334  - end of helix
    Processing helix  chain 'A' and resid 352 through 362
      removed outlier: 3.539A  pdb=" N   LEU A 356 " --> pdb=" O   ASP A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 411
      removed outlier: 3.793A  pdb=" N   MET A 397 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLU A 398 " --> pdb=" O   THR A 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 33
    Processing helix  chain 'B' and resid 35 through 63
      removed outlier: 3.512A  pdb=" N   ARG B  63 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 106
      removed outlier: 3.715A  pdb=" N   GLU B  78 " --> pdb=" O   TRP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 134
    Processing helix  chain 'B' and resid 239 through 273
    Processing helix  chain 'B' and resid 310 through 315
      removed outlier: 4.238A  pdb=" N   LEU B 314 " --> pdb=" O   PRO B 310 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   TYR B 315 " --> pdb=" O   CYS B 311 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 310 through 315'
    Processing helix  chain 'B' and resid 315 through 343
      removed outlier: 3.622A  pdb=" N   THR B 319 " --> pdb=" O   TYR B 315 " (cutoff:3.500A)
      Proline residue:  B 334  - end of helix
    Processing helix  chain 'B' and resid 352 through 363
      removed outlier: 3.539A  pdb=" N   LEU B 356 " --> pdb=" O   ASP B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 411
      removed outlier: 3.793A  pdb=" N   MET B 397 " --> pdb=" O   PRO B 393 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   GLU B 398 " --> pdb=" O   THR B 394 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 377
      removed outlier: 6.056A  pdb=" N   GLU A 371 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   HIS A 387 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   ARG A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA A 414 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 370 through 377
      removed outlier: 6.046A  pdb=" N   GLU B 371 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   HIS B 387 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ARG B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ALA B 414 " --> pdb=" O   ILE B 382 " (cutoff:3.500A)

    351 hydrogen bonds defined for protein.
    1053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 748
        1.28 -     1.42: 1281
        1.42 -     1.55: 2759
        1.55 -     1.68: 2
        1.68 -     1.82: 60
  Bond restraints: 4850
  Sorted by residual:
  bond pdb=" CA  TRP A 375 "
       pdb=" C   TRP A 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.399  0.122 1.24e-02 6.50e+03 9.65e+01
  bond pdb=" CA  TRP B 375 "
       pdb=" C   TRP B 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.401  0.120 1.24e-02 6.50e+03 9.41e+01
  bond pdb=" CA  LEU A 372 "
       pdb=" C   LEU A 372 "
    ideal  model  delta    sigma   weight residual
    1.524  1.410  0.114 1.23e-02 6.61e+03 8.55e+01
  bond pdb=" CA  LEU B 372 "
       pdb=" C   LEU B 372 "
    ideal  model  delta    sigma   weight residual
    1.524  1.410  0.114 1.23e-02 6.61e+03 8.53e+01
  bond pdb=" CA  ALA A  54 "
       pdb=" C   ALA A  54 "
    ideal  model  delta    sigma   weight residual
    1.522  1.393  0.129 1.40e-02 5.10e+03 8.46e+01
  ... (remaining 4845 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.72: 6224
        3.72 -     7.43: 303
        7.43 -    11.15: 66
       11.15 -    14.86: 8
       14.86 -    18.58: 3
  Bond angle restraints: 6604
  Sorted by residual:
  angle pdb=" N   VAL B  56 "
        pdb=" CA  VAL B  56 "
        pdb=" C   VAL B  56 "
      ideal   model   delta    sigma   weight residual
     110.72   92.14   18.58 1.01e+00 9.80e-01 3.38e+02
  angle pdb=" N   LYS A  69 "
        pdb=" CA  LYS A  69 "
        pdb=" C   LYS A  69 "
      ideal   model   delta    sigma   weight residual
     114.31   98.58   15.73 1.29e+00 6.01e-01 1.49e+02
  angle pdb=" N   HIS A  43 "
        pdb=" CA  HIS A  43 "
        pdb=" C   HIS A  43 "
      ideal   model   delta    sigma   weight residual
     113.01  100.68   12.33 1.20e+00 6.94e-01 1.06e+02
  angle pdb=" N   VAL A  56 "
        pdb=" CA  VAL A  56 "
        pdb=" C   VAL A  56 "
      ideal   model   delta    sigma   weight residual
     111.89   97.80   14.09 1.44e+00 4.82e-01 9.58e+01
  angle pdb=" N   LYS B  69 "
        pdb=" CA  LYS B  69 "
        pdb=" C   LYS B  69 "
      ideal   model   delta    sigma   weight residual
     113.61   99.82   13.79 1.50e+00 4.44e-01 8.46e+01
  ... (remaining 6599 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 2494
       15.99 -    31.99: 249
       31.99 -    47.98: 63
       47.98 -    63.98: 18
       63.98 -    79.97: 9
  Dihedral angle restraints: 2833
    sinusoidal: 1037
      harmonic: 1796
  Sorted by residual:
  dihedral pdb=" CB  CYS A 291 "
           pdb=" SG  CYS A 291 "
           pdb=" SG  CYS B 291 "
           pdb=" CB  CYS B 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.51   76.51     1      1.00e+01 1.00e-02 7.36e+01
  dihedral pdb=" CB  CYS A 286 "
           pdb=" SG  CYS A 286 "
           pdb=" SG  CYS A 311 "
           pdb=" CB  CYS A 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -23.94  -62.06     1      1.00e+01 1.00e-02 5.10e+01
  dihedral pdb=" CB  CYS B 286 "
           pdb=" SG  CYS B 286 "
           pdb=" SG  CYS B 311 "
           pdb=" CB  CYS B 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -23.98  -62.02     1      1.00e+01 1.00e-02 5.10e+01
  ... (remaining 2830 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 663
       0.098 -    0.197: 94
       0.197 -    0.295: 24
       0.295 -    0.394: 10
       0.394 -    0.492: 8
  Chirality restraints: 799
  Sorted by residual:
  chirality pdb=" CA  TRP B  74 "
            pdb=" N   TRP B  74 "
            pdb=" C   TRP B  74 "
            pdb=" CB  TRP B  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.06e+00
  chirality pdb=" CA  HIS A 408 "
            pdb=" N   HIS A 408 "
            pdb=" C   HIS A 408 "
            pdb=" CB  HIS A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.86e+00
  chirality pdb=" CA  HIS B 408 "
            pdb=" N   HIS B 408 "
            pdb=" C   HIS B 408 "
            pdb=" CB  HIS B 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.83e+00
  ... (remaining 796 not shown)

  Planarity restraints: 825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 336 "    0.041 2.00e-02 2.50e+03   8.23e-02 6.77e+01
        pdb=" C   LEU A 336 "   -0.142 2.00e-02 2.50e+03
        pdb=" O   LEU A 336 "    0.053 2.00e-02 2.50e+03
        pdb=" N   LYS A 337 "    0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 336 "   -0.041 2.00e-02 2.50e+03   8.22e-02 6.76e+01
        pdb=" C   LEU B 336 "    0.142 2.00e-02 2.50e+03
        pdb=" O   LEU B 336 "   -0.053 2.00e-02 2.50e+03
        pdb=" N   LYS B 337 "   -0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 411 "   -0.040 2.00e-02 2.50e+03   7.79e-02 6.07e+01
        pdb=" C   GLY A 411 "    0.135 2.00e-02 2.50e+03
        pdb=" O   GLY A 411 "   -0.050 2.00e-02 2.50e+03
        pdb=" N   ILE A 412 "   -0.045 2.00e-02 2.50e+03
  ... (remaining 822 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.28: 22
        2.28 -     2.93: 2485
        2.93 -     3.59: 7490
        3.59 -     4.24: 10516
        4.24 -     4.90: 17643
  Nonbonded interactions: 38156
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 420 "
            pdb="ZN    ZN B 601 "
     model   vdw
     1.624 2.230
  nonbonded pdb=" OE2 GLU A 420 "
            pdb="ZN    ZN A 601 "
     model   vdw
     1.659 2.230
  nonbonded pdb=" OD1 ASP A 255 "
            pdb="ZN    ZN A 602 "
     model   vdw
     1.782 2.230
  nonbonded pdb=" OD1 ASP B 255 "
            pdb="ZN    ZN B 602 "
     model   vdw
     1.792 2.230
  nonbonded pdb=" OE1 GLU B 371 "
            pdb="ZN    ZN B 603 "
     model   vdw
     1.851 2.230
  ... (remaining 38151 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 361 or (resid 362 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 363 through 366 or (resid 367 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 368 through 421 or resid 601 \ 
 through 604))
  selection = (chain 'B' and (resid 5 through 353 or (resid 354 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 355 through 360 or (resid 361 through 362 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 363 through 381  \ 
or (resid 382 and (name N or name CA or name C or name O or name CB )) or resid  \ 
383 through 388 or (resid 389 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 390 through 396 or (resid 397 through 398 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 399 through 403 or (resid 404 throug \ 
h 405 and (name N or name CA or name C or name O or name CB )) or resid 406 thro \ 
ugh 421 or resid 601 through 604))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.090
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
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      :  0.017   0.129   4850  Z= 1.144
  Angle     :  1.805  18.578   6604  Z= 1.231
  Chirality :  0.094   0.492    799
  Planarity :  0.012   0.082    825
  Dihedral  : 14.915  79.971   1654
  Min Nonbonded Distance : 1.624

Molprobity Statistics.
  All-atom Clashscore : 28.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  5.05 %
    Favored  : 92.32 %
  Cbeta Deviations :  1.55 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.35), residues: 614
  helix:  0.74 (0.25), residues: 404
  sheet: -0.56 (0.85), residues: 44
  loop : -1.58 (0.53), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.005   TRP A 375 
 HIS   0.053   0.007   HIS A 146 
 PHE   0.027   0.002   PHE B  72 
 TYR   0.009   0.001   TYR B 396 
 ARG   0.004   0.000   ARG B  62 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8360 (mmt) cc_final: 0.8077 (mmt)
REVERT: A   46 SER cc_start: 0.8443 (m) cc_final: 0.8179 (t)
REVERT: A   62 ARG cc_start: 0.8217 (mmt180) cc_final: 0.8005 (mtp-110)
REVERT: A  287 PHE cc_start: 0.8941 (t80) cc_final: 0.8574 (t80)
REVERT: A  289 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8081 (m-30)
REVERT: A  324 MET cc_start: 0.8106 (tmm) cc_final: 0.7676 (tmm)
REVERT: A  370 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.5971 (p90)
REVERT: A  409 ASN cc_start: 0.9068 (t0) cc_final: 0.8818 (m-40)
REVERT: B   49 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8031 (tp)
REVERT: B  287 PHE cc_start: 0.8989 (t80) cc_final: 0.8625 (t80)
REVERT: B  289 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8093 (m-30)
REVERT: B  324 MET cc_start: 0.8139 (tmm) cc_final: 0.7702 (tmm)
  outliers start: 13
  outliers final: 4
  residues processed: 169
  average time/residue: 0.1398
  time to fit residues: 30.7313
Evaluate side-chains
  142 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  146 HIS
Chi-restraints excluded: chain B residue  289 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 18 optimal weight:   30.0000
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 155 HIS
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 ASN
A 410 HIS
A 413 HIS
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 HIS
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 408 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.214509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.156319 restraints weight = 5271.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.160528 restraints weight = 3909.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.162823 restraints weight = 3257.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4850  Z= 0.290
  Angle     :  0.715   8.585   6604  Z= 0.383
  Chirality :  0.046   0.177    799
  Planarity :  0.005   0.048    825
  Dihedral  :  5.861  56.466    672
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.12 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 13.94 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.35), residues: 614
  helix:  1.60 (0.24), residues: 404
  sheet: -2.13 (0.65), residues: 44
  loop : -0.85 (0.58), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 375 
 HIS   0.037   0.004   HIS A 148 
 PHE   0.029   0.001   PHE A 421 
 TYR   0.013   0.002   TYR A 396 
 ARG   0.005   0.001   ARG B  76 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.6573 (OUTLIER) cc_final: 0.5955 (mp)
REVERT: A  287 PHE cc_start: 0.9032 (t80) cc_final: 0.8798 (t80)
REVERT: A  289 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7047 (t0)
REVERT: A  409 ASN cc_start: 0.8376 (t0) cc_final: 0.8125 (m-40)
REVERT: B   75 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6314 (mp)
REVERT: B  287 PHE cc_start: 0.9068 (t80) cc_final: 0.8813 (t80)
REVERT: B  289 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.6977 (t0)
REVERT: B  320 LEU cc_start: 0.8536 (mt) cc_final: 0.8278 (mt)
  outliers start: 23
  outliers final: 10
  residues processed: 154
  average time/residue: 0.1258
  time to fit residues: 25.8315
Evaluate side-chains
  148 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   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 146 HIS
A 155 HIS
A 410 HIS
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 HIS
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.215176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.156339 restraints weight = 5194.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.159964 restraints weight = 3888.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.162864 restraints weight = 3256.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4850  Z= 0.247
  Angle     :  0.624   6.035   6604  Z= 0.334
  Chirality :  0.045   0.139    799
  Planarity :  0.004   0.034    825
  Dihedral  :  4.646  22.175    662
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 16.97 %
    Favored  : 77.98 %
  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:  1.37 (0.36), residues: 614
  helix:  1.83 (0.24), residues: 406
  sheet: -1.72 (0.77), residues: 40
  loop : -0.62 (0.60), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  74 
 HIS   0.040   0.003   HIS B 148 
 PHE   0.020   0.001   PHE A 421 
 TYR   0.014   0.002   TYR A 396 
 ARG   0.003   0.000   ARG A  59 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7564 (mmp) cc_final: 0.7047 (mpp)
REVERT: A   75 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6030 (mp)
REVERT: A  115 VAL cc_start: 0.9026 (m) cc_final: 0.8808 (p)
REVERT: A  124 LEU cc_start: 0.7848 (tt) cc_final: 0.7642 (tt)
REVERT: A  396 TYR cc_start: 0.7826 (t80) cc_final: 0.7565 (t80)
REVERT: A  410 HIS cc_start: 0.8181 (m-70) cc_final: 0.7876 (m170)
REVERT: B   75 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6307 (mp)
REVERT: B  115 VAL cc_start: 0.9024 (m) cc_final: 0.8814 (p)
REVERT: B  124 LEU cc_start: 0.7861 (tt) cc_final: 0.7645 (tt)
REVERT: B  368 GLU cc_start: 0.8407 (pt0) cc_final: 0.7843 (pm20)
REVERT: B  404 LYS cc_start: 0.8696 (tppt) cc_final: 0.8399 (mmmm)
REVERT: B  409 ASN cc_start: 0.8480 (m-40) cc_final: 0.8208 (m-40)
  outliers start: 25
  outliers final: 16
  residues processed: 155
  average time/residue: 0.1279
  time to fit residues: 26.3682
Evaluate side-chains
  143 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 155 HIS
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 HIS
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.214376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.155519 restraints weight = 5056.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.159456 restraints weight = 3847.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.162068 restraints weight = 3245.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.3556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4850  Z= 0.238
  Angle     :  0.619   6.981   6604  Z= 0.327
  Chirality :  0.044   0.159    799
  Planarity :  0.004   0.033    825
  Dihedral  :  4.314  21.427    658
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 19.39 %
    Favored  : 75.76 %
  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:  1.48 (0.35), residues: 614
  helix:  1.96 (0.25), residues: 406
  sheet: -1.48 (0.81), residues: 38
  loop : -0.80 (0.56), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  74 
 HIS   0.043   0.003   HIS B 148 
 PHE   0.007   0.001   PHE B  94 
 TYR   0.014   0.001   TYR A 396 
 ARG   0.003   0.000   ARG A  62 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.5995 (mp)
REVERT: A  115 VAL cc_start: 0.9007 (m) cc_final: 0.8796 (p)
REVERT: A  420 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7896 (tt0)
REVERT: B   75 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6194 (mp)
REVERT: B  115 VAL cc_start: 0.9015 (m) cc_final: 0.8804 (p)
REVERT: B  368 GLU cc_start: 0.8368 (pt0) cc_final: 0.7939 (pm20)
REVERT: B  404 LYS cc_start: 0.8621 (tppt) cc_final: 0.8324 (mmmm)
REVERT: B  409 ASN cc_start: 0.8429 (m-40) cc_final: 0.8081 (m-40)
REVERT: B  420 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8161 (tt0)
  outliers start: 24
  outliers final: 15
  residues processed: 137
  average time/residue: 0.1406
  time to fit residues: 25.2839
Evaluate side-chains
  144 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 155 HIS
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.214128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.155417 restraints weight = 5428.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.159147 restraints weight = 4111.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.161780 restraints weight = 3477.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4850  Z= 0.267
  Angle     :  0.598   7.998   6604  Z= 0.321
  Chirality :  0.044   0.225    799
  Planarity :  0.004   0.032    825
  Dihedral  :  4.257  20.854    658
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 21.21 %
    Favored  : 72.12 %
  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:  1.41 (0.35), residues: 614
  helix:  1.88 (0.25), residues: 406
  sheet: -1.38 (0.83), residues: 38
  loop : -0.79 (0.56), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 375 
 HIS   0.038   0.003   HIS B 148 
 PHE   0.009   0.001   PHE B 287 
 TYR   0.019   0.002   TYR B 396 
 ARG   0.003   0.000   ARG B  76 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6292 (mp)
REVERT: A  115 VAL cc_start: 0.9030 (m) cc_final: 0.8821 (p)
REVERT: A  289 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6827 (t0)
REVERT: A  312 TRP cc_start: 0.8688 (p-90) cc_final: 0.8120 (p-90)
REVERT: A  420 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7731 (tt0)
REVERT: B   42 PHE cc_start: 0.7927 (m-80) cc_final: 0.7589 (m-80)
REVERT: B   75 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6428 (mp)
REVERT: B  289 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6809 (t0)
REVERT: B  312 TRP cc_start: 0.8646 (p-90) cc_final: 0.8096 (p-90)
REVERT: B  368 GLU cc_start: 0.8270 (pt0) cc_final: 0.7951 (pm20)
REVERT: B  404 LYS cc_start: 0.8647 (tppt) cc_final: 0.8338 (mmmm)
REVERT: B  420 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8121 (tt0)
  outliers start: 33
  outliers final: 19
  residues processed: 148
  average time/residue: 0.1431
  time to fit residues: 27.6447
Evaluate side-chains
  149 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 51 optimal weight:    0.0370
   chunk 33 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0970
   chunk 38 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.4054

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

Flipped N/Q/H residues before XYZ refinement:
A 408 HIS
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.216577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.159483 restraints weight = 5379.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.163568 restraints weight = 4014.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.166072 restraints weight = 3360.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4850  Z= 0.194
  Angle     :  0.560   6.219   6604  Z= 0.301
  Chirality :  0.042   0.152    799
  Planarity :  0.003   0.030    825
  Dihedral  :  4.214  23.005    658
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 23.84 %
    Favored  : 70.71 %
  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:  1.67 (0.35), residues: 614
  helix:  2.14 (0.25), residues: 406
  sheet: -1.36 (0.83), residues: 38
  loop : -0.86 (0.55), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  74 
 HIS   0.037   0.002   HIS B 148 
 PHE   0.020   0.001   PHE A  42 
 TYR   0.023   0.002   TYR A 396 
 ARG   0.002   0.000   ARG A  59 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 VAL cc_start: 0.8997 (m) cc_final: 0.8793 (p)
REVERT: A  312 TRP cc_start: 0.8614 (p-90) cc_final: 0.7952 (p-90)
REVERT: A  420 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7657 (tt0)
REVERT: B   42 PHE cc_start: 0.7780 (m-80) cc_final: 0.7457 (m-80)
REVERT: B   75 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6078 (mp)
REVERT: B  312 TRP cc_start: 0.8643 (p-90) cc_final: 0.7982 (p-90)
REVERT: B  368 GLU cc_start: 0.8131 (pt0) cc_final: 0.7914 (pm20)
REVERT: B  404 LYS cc_start: 0.8641 (tppt) cc_final: 0.8356 (mmmm)
REVERT: B  420 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8001 (tt0)
  outliers start: 27
  outliers final: 19
  residues processed: 144
  average time/residue: 0.1405
  time to fit residues: 26.5068
Evaluate side-chains
  151 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  408 HIS
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   chunk 32 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 54 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 408 HIS
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.214884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.157896 restraints weight = 5374.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.161918 restraints weight = 4035.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.164368 restraints weight = 3393.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4850  Z= 0.225
  Angle     :  0.567   7.202   6604  Z= 0.305
  Chirality :  0.042   0.142    799
  Planarity :  0.004   0.030    825
  Dihedral  :  4.179  23.584    658
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 23.43 %
    Favored  : 70.30 %
  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:  1.68 (0.35), residues: 614
  helix:  2.14 (0.24), residues: 406
  sheet: -1.30 (0.85), residues: 38
  loop : -0.84 (0.55), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B  74 
 HIS   0.034   0.002   HIS B 148 
 PHE   0.015   0.001   PHE A  42 
 TYR   0.029   0.002   TYR A 396 
 ARG   0.002   0.000   ARG B  76 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 TRP cc_start: 0.8622 (p-90) cc_final: 0.8001 (p-90)
REVERT: A  420 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7498 (tt0)
REVERT: B   42 PHE cc_start: 0.7819 (m-80) cc_final: 0.7513 (m-80)
REVERT: B   75 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6181 (mp)
REVERT: B  312 TRP cc_start: 0.8658 (p-90) cc_final: 0.8030 (p-90)
REVERT: B  368 GLU cc_start: 0.8109 (pt0) cc_final: 0.7896 (pm20)
REVERT: B  404 LYS cc_start: 0.8646 (tppt) cc_final: 0.8351 (mmmm)
REVERT: B  420 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8052 (tt0)
  outliers start: 31
  outliers final: 19
  residues processed: 143
  average time/residue: 0.1349
  time to fit residues: 25.6240
Evaluate side-chains
  142 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 58 optimal weight:    0.1980
   chunk 26 optimal weight:    0.4980
   chunk 29 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 370 HIS
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.216742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.159896 restraints weight = 5330.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.164041 restraints weight = 3999.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.166021 restraints weight = 3344.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4850  Z= 0.209
  Angle     :  0.584   7.726   6604  Z= 0.310
  Chirality :  0.042   0.140    799
  Planarity :  0.003   0.024    825
  Dihedral  :  4.185  29.699    658
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 24.44 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.35), residues: 614
  helix:  2.23 (0.25), residues: 406
  sheet: -1.29 (0.86), residues: 38
  loop : -0.83 (0.54), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B  74 
 HIS   0.011   0.002   HIS B 146 
 PHE   0.009   0.001   PHE A 421 
 TYR   0.035   0.002   TYR A 396 
 ARG   0.002   0.000   ARG B  76 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7706 (mtm-85)
REVERT: A   68 GLN cc_start: 0.7512 (tt0) cc_final: 0.7232 (tt0)
REVERT: A   75 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.5973 (mp)
REVERT: A  157 HIS cc_start: 0.5845 (p-80) cc_final: 0.5263 (p-80)
REVERT: A  312 TRP cc_start: 0.8632 (p-90) cc_final: 0.8017 (p-90)
REVERT: A  420 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7502 (tt0)
REVERT: B   75 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6041 (mp)
REVERT: B  312 TRP cc_start: 0.8655 (p-90) cc_final: 0.8045 (p-90)
REVERT: B  404 LYS cc_start: 0.8588 (tppt) cc_final: 0.8356 (mmmm)
  outliers start: 28
  outliers final: 17
  residues processed: 139
  average time/residue: 0.1483
  time to fit residues: 27.1098
Evaluate side-chains
  142 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  385 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 HIS
B 148 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.214088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.156997 restraints weight = 5369.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.161279 restraints weight = 3994.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.163995 restraints weight = 3307.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4850  Z= 0.232
  Angle     :  0.589   8.290   6604  Z= 0.313
  Chirality :  0.043   0.151    799
  Planarity :  0.003   0.024    825
  Dihedral  :  4.162  23.908    658
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 24.85 %
    Favored  : 70.51 %
  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:  1.41 (0.34), residues: 614
  helix:  1.94 (0.24), residues: 418
  sheet: -1.26 (0.85), residues: 38
  loop : -1.24 (0.52), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  74 
 HIS   0.010   0.002   HIS B 148 
 PHE   0.008   0.001   PHE A 421 
 TYR   0.025   0.002   TYR A 396 
 ARG   0.007   0.000   ARG B  62 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6429 (mpp)
REVERT: A   68 GLN cc_start: 0.7478 (tt0) cc_final: 0.7177 (tt0)
REVERT: A   75 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6028 (mp)
REVERT: A  289 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6716 (t70)
REVERT: A  312 TRP cc_start: 0.8659 (p-90) cc_final: 0.8050 (p-90)
REVERT: A  324 MET cc_start: 0.7870 (tmm) cc_final: 0.7617 (ttp)
REVERT: A  420 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7466 (tt0)
REVERT: B   75 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6103 (mp)
REVERT: B  312 TRP cc_start: 0.8692 (p-90) cc_final: 0.8074 (p-90)
REVERT: B  404 LYS cc_start: 0.8446 (tppt) cc_final: 0.8224 (mmmm)
  outliers start: 23
  outliers final: 15
  residues processed: 142
  average time/residue: 0.1393
  time to fit residues: 26.3021
Evaluate side-chains
  138 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  385 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 49 optimal weight:    0.1980
   chunk 8 optimal weight:    0.5980
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.215737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.159508 restraints weight = 5371.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.163732 restraints weight = 4019.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.166456 restraints weight = 3344.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4850  Z= 0.220
  Angle     :  0.607   8.623   6604  Z= 0.323
  Chirality :  0.043   0.140    799
  Planarity :  0.004   0.024    825
  Dihedral  :  4.299  28.511    658
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 25.25 %
    Favored  : 70.30 %
  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:  1.36 (0.34), residues: 614
  helix:  1.93 (0.24), residues: 418
  sheet: -1.49 (0.81), residues: 42
  loop : -1.27 (0.52), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B  74 
 HIS   0.019   0.002   HIS B 148 
 PHE   0.007   0.001   PHE A 421 
 TYR   0.031   0.002   TYR A 396 
 ARG   0.005   0.000   ARG B  62 

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

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

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1228 Ramachandran restraints generated.
    614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6344 (mpp)
REVERT: A   68 GLN cc_start: 0.7403 (tt0) cc_final: 0.7154 (tt0)
REVERT: A   75 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.5933 (mp)
REVERT: A  312 TRP cc_start: 0.8782 (p-90) cc_final: 0.8222 (p-90)
REVERT: A  410 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7425 (t-90)
REVERT: A  420 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7452 (tt0)
REVERT: B   42 PHE cc_start: 0.7732 (m-80) cc_final: 0.7467 (m-80)
REVERT: B   75 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6033 (mp)
REVERT: B  312 TRP cc_start: 0.8699 (p-90) cc_final: 0.8116 (p-90)
REVERT: B  396 TYR cc_start: 0.7419 (t80) cc_final: 0.7204 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 136
  average time/residue: 0.1302
  time to fit residues: 23.6368
Evaluate side-chains
  145 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  385 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 19 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   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 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.216477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.157657 restraints weight = 5439.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.162175 restraints weight = 3927.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.164583 restraints weight = 3212.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4850  Z= 0.237
  Angle     :  0.618   8.675   6604  Z= 0.326
  Chirality :  0.043   0.142    799
  Planarity :  0.004   0.024    825
  Dihedral  :  4.435  37.303    658
  Min Nonbonded Distance : 1.431

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 25.05 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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:  1.54 (0.34), residues: 614
  helix:  2.06 (0.24), residues: 406
  sheet: -1.38 (0.82), residues: 42
  loop : -0.94 (0.53), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  74 
 HIS   0.017   0.002   HIS A 387 
 PHE   0.008   0.001   PHE B  94 
 TYR   0.017   0.001   TYR A 396 
 ARG   0.004   0.000   ARG A  62 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1710.12 seconds
wall clock time: 31 minutes 17.72 seconds (1877.72 seconds total)