Starting phenix.real_space_refine
on Thu Mar  6 03:37:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zsz_60435/03_2025/8zsz_60435.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zsz_60435/03_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_60435/03_2025/8zsz_60435.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zsz_60435/03_2025/8zsz_60435.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zsz_60435/03_2025/8zsz_60435.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zsz_60435/03_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-5624/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: 3.49, per 1000 atoms: 0.73
  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: 1.26
  Conformation dependent library (CDL) restraints added in 578.0 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: 0.33
  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: 1.17

  Time building geometry restraints manager: 1.51 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:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.320
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.310
-------------------------------------------------------------------------------
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  : 0.489 
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: 0.1375
  time to fit residues: 30.4135
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  : 0.497 
-------------------------------------------------------------------------------
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 = 40)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.156319 restraints weight = 5271.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.160527 restraints weight = 3909.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.162776 restraints weight = 3250.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
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  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.5959 (mp)
REVERT: A  287 PHE cc_start: 0.9028 (t80) cc_final: 0.8796 (t80)
REVERT: A  289 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7046 (t0)
REVERT: A  409 ASN cc_start: 0.8374 (t0) cc_final: 0.8124 (m-40)
REVERT: B   75 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6318 (mp)
REVERT: B  287 PHE cc_start: 0.9064 (t80) cc_final: 0.8811 (t80)
REVERT: B  289 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.6975 (t0)
REVERT: B  320 LEU cc_start: 0.8533 (mt) cc_final: 0.8277 (mt)
  outliers start: 23
  outliers final: 10
  residues processed: 154
  average time/residue: 0.1284
  time to fit residues: 26.3548
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  : 0.475 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4417 r_free = 0.4417 target = 0.216975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.155300 restraints weight = 5132.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.159645 restraints weight = 3746.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.162010 restraints weight = 3087.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4850  Z= 0.238
  Angle     :  0.619   5.868   6604  Z= 0.331
  Chirality :  0.044   0.138    799
  Planarity :  0.004   0.031    825
  Dihedral  :  4.649  23.407    662
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 16.97 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.36), residues: 614
  helix:  1.85 (0.24), residues: 406
  sheet: -1.71 (0.77), residues: 40
  loop : -0.61 (0.60), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.036   0.003   HIS B 148 
 PHE   0.017   0.001   PHE A 421 
 TYR   0.014   0.002   TYR A 396 
 ARG   0.004   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
  168 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7613 (mmp) cc_final: 0.7037 (mpp)
REVERT: A   75 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.5854 (mp)
REVERT: A  115 VAL cc_start: 0.9032 (m) cc_final: 0.8815 (p)
REVERT: A  124 LEU cc_start: 0.7774 (tt) cc_final: 0.7557 (tt)
REVERT: A  396 TYR cc_start: 0.7871 (t80) cc_final: 0.7593 (t80)
REVERT: A  410 HIS cc_start: 0.8242 (m-70) cc_final: 0.7930 (m170)
REVERT: B   75 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6239 (mp)
REVERT: B  115 VAL cc_start: 0.9040 (m) cc_final: 0.8829 (p)
REVERT: B  368 GLU cc_start: 0.8420 (pt0) cc_final: 0.7799 (pm20)
REVERT: B  404 LYS cc_start: 0.8699 (tppt) cc_final: 0.8405 (mmmm)
REVERT: B  409 ASN cc_start: 0.8492 (m-40) cc_final: 0.8226 (m-40)
  outliers start: 26
  outliers final: 16
  residues processed: 154
  average time/residue: 0.1299
  time to fit residues: 26.5061
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  : 0.544 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 14 optimal weight:    7.9990
   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 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 = 0.4426 r_free = 0.4426 target = 0.217082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.155178 restraints weight = 4956.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.159161 restraints weight = 3672.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.161885 restraints weight = 3081.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3562

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= 0.234
  Angle     :  0.611   6.783   6604  Z= 0.323
  Chirality :  0.044   0.144    799
  Planarity :  0.004   0.035    825
  Dihedral  :  4.314  21.139    658
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 18.38 %
    Favored  : 76.77 %
  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:  1.97 (0.25), residues: 406
  sheet: -1.46 (0.82), residues: 38
  loop : -0.85 (0.56), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  74 
 HIS   0.041   0.003   HIS B 148 
 PHE   0.012   0.001   PHE B 287 
 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
  157 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.6514 (OUTLIER) cc_final: 0.5918 (mp)
REVERT: A  115 VAL cc_start: 0.9010 (m) cc_final: 0.8803 (p)
REVERT: A  420 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7920 (tt0)
REVERT: B   75 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6135 (mp)
REVERT: B  115 VAL cc_start: 0.9020 (m) cc_final: 0.8817 (p)
REVERT: B  312 TRP cc_start: 0.8603 (p-90) cc_final: 0.8023 (p-90)
REVERT: B  368 GLU cc_start: 0.8391 (pt0) cc_final: 0.7923 (pm20)
REVERT: B  404 LYS cc_start: 0.8618 (tppt) cc_final: 0.8326 (mmmm)
REVERT: B  409 ASN cc_start: 0.8430 (m-40) cc_final: 0.8036 (m-40)
  outliers start: 24
  outliers final: 14
  residues processed: 144
  average time/residue: 0.1428
  time to fit residues: 27.0718
Evaluate side-chains
  142 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
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   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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 36 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 413 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 = 0.4399 r_free = 0.4399 target = 0.212744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.154147 restraints weight = 5405.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.158082 restraints weight = 4033.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.160740 restraints weight = 3374.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4850  Z= 0.269
  Angle     :  0.601   8.127   6604  Z= 0.323
  Chirality :  0.045   0.221    799
  Planarity :  0.004   0.031    825
  Dihedral  :  4.261  21.386    658
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 22.02 %
    Favored  : 71.92 %
  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:  1.43 (0.35), residues: 614
  helix:  1.89 (0.25), residues: 406
  sheet: -1.22 (0.84), residues: 38
  loop : -0.82 (0.56), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 375 
 HIS   0.041   0.003   HIS B 148 
 PHE   0.009   0.001   PHE A 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
  158 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6328 (mp)
REVERT: A  115 VAL cc_start: 0.9007 (m) cc_final: 0.8796 (p)
REVERT: A  289 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6809 (t0)
REVERT: A  312 TRP cc_start: 0.8661 (p-90) cc_final: 0.8126 (p-90)
REVERT: A  420 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7689 (tt0)
REVERT: B   42 PHE cc_start: 0.7895 (m-80) cc_final: 0.7543 (m-80)
REVERT: B   75 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6480 (mp)
REVERT: B  289 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6793 (t0)
REVERT: B  312 TRP cc_start: 0.8623 (p-90) cc_final: 0.8085 (p-90)
REVERT: B  368 GLU cc_start: 0.8183 (pt0) cc_final: 0.7980 (pm20)
REVERT: B  404 LYS cc_start: 0.8656 (tppt) cc_final: 0.8350 (mmmm)
  outliers start: 30
  outliers final: 19
  residues processed: 144
  average time/residue: 0.1447
  time to fit residues: 27.0806
Evaluate side-chains
  146 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
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  110 MET
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   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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 51 optimal weight:    0.4980
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0670
   chunk 38 optimal weight:    0.0770
   chunk 37 optimal weight:    0.0970
   overall best weight:    0.3074

-------------------------------------------------------------------------------
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**
** B 345 GLN ** 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 = 0.4441 r_free = 0.4441 target = 0.216962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.159945 restraints weight = 5362.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.164202 restraints weight = 3967.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.166428 restraints weight = 3290.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.4084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4850  Z= 0.179
  Angle     :  0.553   6.438   6604  Z= 0.297
  Chirality :  0.042   0.137    799
  Planarity :  0.003   0.027    825
  Dihedral  :  4.190  23.422    658
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 23.84 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.35), residues: 614
  helix:  2.23 (0.25), residues: 406
  sheet: -1.22 (0.85), residues: 38
  loop : -0.88 (0.54), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 312 
 HIS   0.031   0.002   HIS B 148 
 PHE   0.022   0.001   PHE A  42 
 TYR   0.023   0.001   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
  157 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6825 (t70)
REVERT: A  312 TRP cc_start: 0.8620 (p-90) cc_final: 0.7976 (p-90)
REVERT: A  420 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7607 (tt0)
REVERT: B   75 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.5970 (mp)
REVERT: B  312 TRP cc_start: 0.8626 (p-90) cc_final: 0.7998 (p-90)
REVERT: B  404 LYS cc_start: 0.8640 (tppt) cc_final: 0.8355 (mmmm)
  outliers start: 23
  outliers final: 14
  residues processed: 144
  average time/residue: 0.1386
  time to fit residues: 26.2011
Evaluate side-chains
  146 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
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  272 SER
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  314 LEU
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   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  314 LEU
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 32 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 59 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4422 r_free = 0.4422 target = 0.215841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.156226 restraints weight = 5401.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.160014 restraints weight = 3953.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.163466 restraints weight = 3275.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.4226

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= 0.239
  Angle     :  0.577   7.937   6604  Z= 0.309
  Chirality :  0.043   0.138    799
  Planarity :  0.004   0.028    825
  Dihedral  :  4.155  24.200    658
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 23.84 %
    Favored  : 71.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.35), residues: 614
  helix:  2.16 (0.24), residues: 406
  sheet: -1.18 (0.85), residues: 38
  loop : -0.83 (0.54), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  74 
 HIS   0.033   0.002   HIS B 148 
 PHE   0.018   0.001   PHE A 287 
 TYR   0.029   0.002   TYR A 396 
 ARG   0.003   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
  155 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7845 (m-80) cc_final: 0.7639 (m-80)
REVERT: A  312 TRP cc_start: 0.8642 (p-90) cc_final: 0.8030 (p-90)
REVERT: A  420 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7482 (tt0)
REVERT: B   42 PHE cc_start: 0.7795 (m-80) cc_final: 0.7479 (m-80)
REVERT: B   75 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6255 (mp)
REVERT: B  106 GLU cc_start: 0.8208 (mt-10) cc_final: 0.8001 (mt-10)
REVERT: B  312 TRP cc_start: 0.8675 (p-90) cc_final: 0.8060 (p-90)
REVERT: B  354 ARG cc_start: 0.7974 (mpp80) cc_final: 0.7697 (mpp80)
REVERT: B  404 LYS cc_start: 0.8645 (tppt) cc_final: 0.8357 (mmmm)
  outliers start: 24
  outliers final: 15
  residues processed: 141
  average time/residue: 0.1443
  time to fit residues: 26.6183
Evaluate side-chains
  141 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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  272 SER
Chi-restraints excluded: chain A residue  314 LEU
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  272 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  415 THR
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:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**
A 409 ASN
** B 146 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 = 0.4422 r_free = 0.4422 target = 0.215022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.158254 restraints weight = 5276.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.162397 restraints weight = 3940.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.165026 restraints weight = 3278.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.4347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4850  Z= 0.223
  Angle     :  0.584   7.635   6604  Z= 0.311
  Chirality :  0.043   0.139    799
  Planarity :  0.004   0.024    825
  Dihedral  :  4.238  33.406    658
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 25.66 %
    Favored  : 70.30 %
  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:  1.44 (0.35), residues: 614
  helix:  1.98 (0.24), residues: 418
  sheet: -1.51 (0.81), residues: 42
  loop : -1.20 (0.54), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 375 
 HIS   0.016   0.002   HIS B 148 
 PHE   0.018   0.001   PHE A 287 
 TYR   0.037   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
  147 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6447 (mpp)
REVERT: A   68 GLN cc_start: 0.7509 (tt0) cc_final: 0.7094 (tt0)
REVERT: A   75 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.6047 (mp)
REVERT: A  312 TRP cc_start: 0.8597 (p-90) cc_final: 0.8009 (p-90)
REVERT: A  420 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7630 (tt0)
REVERT: B   75 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6222 (mp)
REVERT: B   97 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7575 (tp)
REVERT: B  106 GLU cc_start: 0.8209 (mt-10) cc_final: 0.8006 (mt-10)
REVERT: B  312 TRP cc_start: 0.8687 (p-90) cc_final: 0.8071 (p-90)
REVERT: B  354 ARG cc_start: 0.7885 (mpp80) cc_final: 0.7564 (mpp80)
REVERT: B  404 LYS cc_start: 0.8597 (tppt) cc_final: 0.8367 (mmmm)
  outliers start: 20
  outliers final: 9
  residues processed: 136
  average time/residue: 0.1516
  time to fit residues: 26.6709
Evaluate side-chains
  133 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   24 LEU
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  314 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  420 GLU
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   97 LEU
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  314 LEU
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:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0060
   chunk 17 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 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 = 0.4428 r_free = 0.4428 target = 0.215068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.158995 restraints weight = 5372.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.163200 restraints weight = 3971.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.165339 restraints weight = 3300.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4850  Z= 0.219
  Angle     :  0.601   8.518   6604  Z= 0.316
  Chirality :  0.043   0.150    799
  Planarity :  0.003   0.024    825
  Dihedral  :  4.185  27.757    658
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 25.66 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.34), residues: 614
  helix:  2.01 (0.24), residues: 418
  sheet: -1.20 (0.87), residues: 38
  loop : -1.16 (0.52), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 312 
 HIS   0.015   0.002   HIS B 148 
 PHE   0.010   0.001   PHE A 421 
 TYR   0.025   0.002   TYR A 396 
 ARG   0.008   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
  140 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6437 (mpp)
REVERT: A   68 GLN cc_start: 0.7457 (tt0) cc_final: 0.7004 (tt0)
REVERT: A   75 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6021 (mp)
REVERT: A  312 TRP cc_start: 0.8649 (p-90) cc_final: 0.8327 (p-90)
REVERT: A  420 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7618 (tt0)
REVERT: B   75 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6216 (mp)
REVERT: B   97 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7629 (tp)
REVERT: B  106 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8036 (mt-10)
REVERT: B  312 TRP cc_start: 0.8664 (p-90) cc_final: 0.8071 (p-90)
REVERT: B  354 ARG cc_start: 0.7885 (mpp80) cc_final: 0.7465 (mpp80)
REVERT: B  404 LYS cc_start: 0.8442 (tppt) cc_final: 0.8230 (mmmm)
  outliers start: 16
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1484
  time to fit residues: 25.3852
Evaluate side-chains
  134 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
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  314 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  420 GLU
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   97 LEU
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  405 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 18 optimal weight:   50.0000
   chunk 49 optimal weight:   50.0000
   chunk 8 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 146 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 = 0.4408 r_free = 0.4408 target = 0.213243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.156627 restraints weight = 5345.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.160696 restraints weight = 4037.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.163315 restraints weight = 3390.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.4537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4850  Z= 0.250
  Angle     :  0.609   9.984   6604  Z= 0.322
  Chirality :  0.044   0.146    799
  Planarity :  0.004   0.024    825
  Dihedral  :  4.168  26.129    658
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 25.66 %
    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:  1.34 (0.34), residues: 614
  helix:  1.90 (0.24), residues: 418
  sheet: -1.42 (0.81), residues: 42
  loop : -1.26 (0.52), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  74 
 HIS   0.014   0.002   HIS B 148 
 PHE   0.023   0.001   PHE A 287 
 TYR   0.028   0.002   TYR A 396 
 ARG   0.005   0.001   ARG A  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
  139 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6421 (mpp)
REVERT: A   68 GLN cc_start: 0.7426 (tt0) cc_final: 0.7160 (tt0)
REVERT: A   75 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6222 (mp)
REVERT: A  312 TRP cc_start: 0.8791 (p-90) cc_final: 0.8479 (p-90)
REVERT: A  410 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7395 (t-90)
REVERT: B   42 PHE cc_start: 0.7775 (m-80) cc_final: 0.7510 (m-80)
REVERT: B   75 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6345 (mp)
REVERT: B  312 TRP cc_start: 0.8794 (p-90) cc_final: 0.8460 (p-90)
REVERT: B  404 LYS cc_start: 0.8481 (tppt) cc_final: 0.8263 (mmmm)
  outliers start: 20
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1482
  time to fit residues: 25.1327
Evaluate side-chains
  134 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue   24 LEU
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  314 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  410 HIS
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  405 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0970
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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

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 = 0.215941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.164291 restraints weight = 5399.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.163637 restraints weight = 4122.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.164398 restraints weight = 3737.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4850  Z= 0.215
  Angle     :  0.604   9.987   6604  Z= 0.316
  Chirality :  0.043   0.147    799
  Planarity :  0.003   0.024    825
  Dihedral  :  4.196  24.824    658
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.67 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.34), residues: 614
  helix:  1.91 (0.24), residues: 418
  sheet: -1.38 (0.81), residues: 42
  loop : -1.31 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B  74 
 HIS   0.008   0.001   HIS A 387 
 PHE   0.014   0.001   PHE A 287 
 TYR   0.012   0.001   TYR B 396 
 ARG   0.005   0.000   ARG A  62 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1757.31 seconds
wall clock time: 31 minutes 16.16 seconds (1876.16 seconds total)