Starting phenix.real_space_refine
on Sun Apr 27 05:51:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zsz_60435/04_2025/8zsz_60435.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zsz_60435/04_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_60435/04_2025/8zsz_60435.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zsz_60435/04_2025/8zsz_60435.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zsz_60435/04_2025/8zsz_60435.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zsz_60435/04_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-5669/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: 3.39, per 1000 atoms: 0.71
  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: 1.38
  Conformation dependent library (CDL) restraints added in 616.5 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: 0.51
  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: 1.25

  Time building geometry restraints manager: 1.60 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:             0.510
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.710
  Find NCS groups from input model:        0.190
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.440
-------------------------------------------------------------------------------
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      :  0.027   0.721   4869  Z= 1.422
  Angle     :  1.806  18.578   6614  Z= 1.230
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17204 (  351)
  hydrogen bonds       : angle       7.70688 ( 1053)
  metal coordination   : bond        0.39086 (   14)
  SS BOND              : bond        0.01058 (    5)
  SS BOND              : angle       1.89073 (   10)
  covalent geometry    : bond        0.01718 ( 4850)
  covalent geometry    : angle       1.80542 ( 6604)

*********************** 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  : 0.561 
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: 0.1473
  time to fit residues: 32.4819
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  : 0.527 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 18 optimal weight:   30.0000
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 373 HIS ** 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 = 0.214427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.155980 restraints weight = 5267.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.160261 restraints weight = 3926.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.162521 restraints weight = 3276.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.121   4869  Z= 0.228
  Angle     :  0.720   8.705   6614  Z= 0.385
  Chirality :  0.046   0.184    799
  Planarity :  0.005   0.049    825
  Dihedral  :  5.861  56.335    672
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.12 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 13.94 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.35), residues: 614
  helix:  1.60 (0.24), residues: 404
  sheet: -2.14 (0.66), residues: 44
  loop : -0.85 (0.58), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 375 
 HIS   0.039   0.004   HIS A 148 
 PHE   0.029   0.001   PHE A 421 
 TYR   0.012   0.002   TYR A 396 
 ARG   0.005   0.001   ARG B  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06071 (  351)
  hydrogen bonds       : angle       5.16816 ( 1053)
  metal coordination   : bond        0.06308 (   14)
  SS BOND              : bond        0.00554 (    5)
  SS BOND              : angle       1.84675 (   10)
  covalent geometry    : bond        0.00425 ( 4850)
  covalent geometry    : angle       0.71645 ( 6604)

*********************** 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
  165 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ARG cc_start: 0.7891 (mmt180) cc_final: 0.7668 (mtm-85)
REVERT: A   75 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.5939 (mp)
REVERT: A  287 PHE cc_start: 0.9042 (t80) cc_final: 0.8797 (t80)
REVERT: A  289 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7052 (t0)
REVERT: A  409 ASN cc_start: 0.8385 (t0) cc_final: 0.8130 (m-40)
REVERT: B   75 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6313 (mp)
REVERT: B  287 PHE cc_start: 0.9081 (t80) cc_final: 0.8816 (t80)
REVERT: B  289 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.6977 (t0)
REVERT: B  320 LEU cc_start: 0.8568 (mt) cc_final: 0.8317 (mt)
  outliers start: 24
  outliers final: 9
  residues processed: 155
  average time/residue: 0.1273
  time to fit residues: 26.3585
Evaluate side-chains
  147 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0670
   chunk 17 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 410 HIS
** B 146 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.217652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.158926 restraints weight = 5244.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.163146 restraints weight = 3877.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.165416 restraints weight = 3231.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4869  Z= 0.161
  Angle     :  0.622   6.037   6614  Z= 0.332
  Chirality :  0.044   0.130    799
  Planarity :  0.004   0.039    825
  Dihedral  :  4.765  24.470    662
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 17.17 %
    Favored  : 77.58 %
  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:  1.44 (0.36), residues: 614
  helix:  1.92 (0.25), residues: 404
  sheet: -1.69 (0.78), residues: 40
  loop : -0.68 (0.59), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  74 
 HIS   0.049   0.004   HIS B 148 
 PHE   0.016   0.001   PHE A 421 
 TYR   0.014   0.001   TYR A 396 
 ARG   0.003   0.000   ARG A  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05099 (  351)
  hydrogen bonds       : angle       4.83177 ( 1053)
  metal coordination   : bond        0.02714 (   14)
  SS BOND              : bond        0.00434 (    5)
  SS BOND              : angle       1.13998 (   10)
  covalent geometry    : bond        0.00325 ( 4850)
  covalent geometry    : angle       0.62101 ( 6604)

*********************** 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
  167 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7592 (mmp) cc_final: 0.7030 (mpp)
REVERT: A   62 ARG cc_start: 0.7946 (mmt180) cc_final: 0.7620 (mtm-85)
REVERT: A   75 ILE cc_start: 0.6351 (OUTLIER) cc_final: 0.5653 (mp)
REVERT: A  115 VAL cc_start: 0.9040 (m) cc_final: 0.8821 (p)
REVERT: A  410 HIS cc_start: 0.8218 (m-70) cc_final: 0.7919 (m170)
REVERT: B   75 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6009 (mp)
REVERT: B  115 VAL cc_start: 0.9043 (m) cc_final: 0.8834 (p)
REVERT: B  404 LYS cc_start: 0.8745 (tppt) cc_final: 0.8446 (mmmm)
REVERT: B  409 ASN cc_start: 0.8461 (m-40) cc_final: 0.8212 (m-40)
  outliers start: 26
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1394
  time to fit residues: 27.8973
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  : 0.501 
-------------------------------------------------------------------------------
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  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  371 GLU
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:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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
** 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 = 0.4427 r_free = 0.4427 target = 0.215940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.156432 restraints weight = 5100.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.160257 restraints weight = 3904.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.162932 restraints weight = 3291.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4869  Z= 0.170
  Angle     :  0.621   6.757   6614  Z= 0.329
  Chirality :  0.044   0.149    799
  Planarity :  0.004   0.035    825
  Dihedral  :  4.458  22.540    658
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 16.97 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.35), residues: 614
  helix:  1.92 (0.25), residues: 406
  sheet: -1.11 (0.85), residues: 38
  loop : -0.87 (0.56), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.040   0.003   HIS B 148 
 PHE   0.008   0.001   PHE A 287 
 TYR   0.020   0.001   TYR A 396 
 ARG   0.002   0.000   ARG A  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04867 (  351)
  hydrogen bonds       : angle       4.71558 ( 1053)
  metal coordination   : bond        0.03494 (   14)
  SS BOND              : bond        0.00645 (    5)
  SS BOND              : angle       2.68868 (   10)
  covalent geometry    : bond        0.00359 ( 4850)
  covalent geometry    : angle       0.61258 ( 6604)

*********************** 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
  162 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ARG cc_start: 0.8048 (mmt180) cc_final: 0.7691 (mtm-85)
REVERT: A   75 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.5932 (mp)
REVERT: A  115 VAL cc_start: 0.9011 (m) cc_final: 0.8800 (p)
REVERT: A  289 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.6911 (t0)
REVERT: A  420 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7922 (tt0)
REVERT: B   42 PHE cc_start: 0.7861 (m-80) cc_final: 0.7500 (m-80)
REVERT: B   75 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6180 (mp)
REVERT: B  115 VAL cc_start: 0.9040 (m) cc_final: 0.8836 (p)
REVERT: B  368 GLU cc_start: 0.8338 (pt0) cc_final: 0.7868 (pm20)
REVERT: B  404 LYS cc_start: 0.8651 (tppt) cc_final: 0.8359 (mmmm)
REVERT: B  409 ASN cc_start: 0.8474 (m-40) cc_final: 0.8096 (m-40)
  outliers start: 30
  outliers final: 18
  residues processed: 145
  average time/residue: 0.1301
  time to fit residues: 25.0612
Evaluate side-chains
  145 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
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  268 VAL
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 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  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  371 GLU
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:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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
** 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 = 0.4400 r_free = 0.4400 target = 0.213113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.158885 restraints weight = 5407.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.160059 restraints weight = 4363.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.161367 restraints weight = 3928.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   4869  Z= 0.189
  Angle     :  0.624   7.674   6614  Z= 0.333
  Chirality :  0.045   0.216    799
  Planarity :  0.004   0.030    825
  Dihedral  :  4.410  22.141    658
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 20.81 %
    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:  1.37 (0.35), residues: 614
  helix:  1.86 (0.25), residues: 406
  sheet: -1.10 (0.89), residues: 38
  loop : -0.93 (0.56), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 375 
 HIS   0.035   0.003   HIS B 148 
 PHE   0.009   0.001   PHE A 287 
 TYR   0.018   0.002   TYR B 396 
 ARG   0.003   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04909 (  351)
  hydrogen bonds       : angle       4.65392 ( 1053)
  metal coordination   : bond        0.03758 (   14)
  SS BOND              : bond        0.00326 (    5)
  SS BOND              : angle       2.06335 (   10)
  covalent geometry    : bond        0.00416 ( 4850)
  covalent geometry    : angle       0.61937 ( 6604)

*********************** 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
  164 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ARG cc_start: 0.8100 (mmt180) cc_final: 0.7772 (mtm-85)
REVERT: A   75 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6255 (mp)
REVERT: A  115 VAL cc_start: 0.9031 (m) cc_final: 0.8823 (p)
REVERT: A  289 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6775 (t0)
REVERT: A  312 TRP cc_start: 0.8698 (p-90) cc_final: 0.8126 (p-90)
REVERT: A  420 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7651 (tt0)
REVERT: B   42 PHE cc_start: 0.7977 (m-80) cc_final: 0.7632 (m-80)
REVERT: B   75 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6522 (mp)
REVERT: B  289 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6691 (t0)
REVERT: B  312 TRP cc_start: 0.8647 (p-90) cc_final: 0.8092 (p-90)
REVERT: B  368 GLU cc_start: 0.8257 (pt0) cc_final: 0.7962 (pm20)
REVERT: B  404 LYS cc_start: 0.8657 (tppt) cc_final: 0.8327 (mmmm)
REVERT: B  409 ASN cc_start: 0.8532 (m-40) cc_final: 0.8314 (m-40)
  outliers start: 35
  outliers final: 19
  residues processed: 147
  average time/residue: 0.1421
  time to fit residues: 27.2912
Evaluate side-chains
  145 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
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  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   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  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:    6.9990
   chunk 33 optimal weight:    0.4980
   chunk 31 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0470
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 HIS
A 413 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.215683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.158007 restraints weight = 5366.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.161919 restraints weight = 4051.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.163977 restraints weight = 3405.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   4869  Z= 0.152
  Angle     :  0.581   7.337   6614  Z= 0.312
  Chirality :  0.043   0.147    799
  Planarity :  0.004   0.032    825
  Dihedral  :  4.360  22.611    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 :  5.66 %
    Allowed  : 22.42 %
    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:  1.65 (0.35), residues: 614
  helix:  2.11 (0.25), residues: 406
  sheet: -1.06 (0.89), residues: 38
  loop : -0.91 (0.54), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 375 
 HIS   0.038   0.003   HIS A 148 
 PHE   0.020   0.001   PHE A  42 
 TYR   0.016   0.002   TYR A 396 
 ARG   0.002   0.000   ARG A  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04519 (  351)
  hydrogen bonds       : angle       4.59898 ( 1053)
  metal coordination   : bond        0.03341 (   14)
  SS BOND              : bond        0.00254 (    5)
  SS BOND              : angle       0.86527 (   10)
  covalent geometry    : bond        0.00307 ( 4850)
  covalent geometry    : angle       0.58091 ( 6604)

*********************** 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: 28
    poor density    : 133
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7821 (mtm-85)
REVERT: A   75 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6064 (mp)
REVERT: A  115 VAL cc_start: 0.8982 (m) cc_final: 0.8780 (p)
REVERT: A  289 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6768 (t0)
REVERT: A  312 TRP cc_start: 0.8636 (p-90) cc_final: 0.8252 (p-90)
REVERT: A  420 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7599 (tt0)
REVERT: B   42 PHE cc_start: 0.7859 (m-80) cc_final: 0.7517 (m-80)
REVERT: B   75 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6292 (mp)
REVERT: B  289 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6782 (t70)
REVERT: B  312 TRP cc_start: 0.8658 (p-90) cc_final: 0.7993 (p-90)
REVERT: B  368 GLU cc_start: 0.8145 (pt0) cc_final: 0.7893 (pm20)
REVERT: B  404 LYS cc_start: 0.8627 (tppt) cc_final: 0.8324 (mmmm)
  outliers start: 28
  outliers final: 19
  residues processed: 147
  average time/residue: 0.1344
  time to fit residues: 25.9770
Evaluate side-chains
  148 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
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   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  272 SER
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  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  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  415 THR
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:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 32 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 HIS
B 127 ASN
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.210044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.152507 restraints weight = 5368.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.156015 restraints weight = 4059.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.158694 restraints weight = 3421.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.338   4869  Z= 0.266
  Angle     :  0.629   6.855   6614  Z= 0.340
  Chirality :  0.045   0.136    799
  Planarity :  0.004   0.038    825
  Dihedral  :  4.386  24.115    658
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  8.08 %
    Allowed  : 21.41 %
    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 (0.35), residues: 614
  helix:  1.91 (0.24), residues: 406
  sheet: -1.35 (0.89), residues: 38
  loop : -0.89 (0.55), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 375 
 HIS   0.043   0.003   HIS A 148 
 PHE   0.013   0.001   PHE A  42 
 TYR   0.023   0.002   TYR A 396 
 ARG   0.004   0.000   ARG B  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04884 (  351)
  hydrogen bonds       : angle       4.62552 ( 1053)
  metal coordination   : bond        0.09725 (   14)
  SS BOND              : bond        0.00378 (    5)
  SS BOND              : angle       0.86480 (   10)
  covalent geometry    : bond        0.00482 ( 4850)
  covalent geometry    : angle       0.62817 ( 6604)

*********************** 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
  165 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 125
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ARG cc_start: 0.8053 (mmt180) cc_final: 0.7783 (mtm-85)
REVERT: A   75 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6444 (mp)
REVERT: A  110 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6650 (ptt)
REVERT: A  115 VAL cc_start: 0.8988 (m) cc_final: 0.8778 (p)
REVERT: A  289 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6748 (t70)
REVERT: A  312 TRP cc_start: 0.8734 (p-90) cc_final: 0.8372 (p-90)
REVERT: A  420 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7622 (tt0)
REVERT: B   42 PHE cc_start: 0.7805 (m-80) cc_final: 0.7460 (m-80)
REVERT: B   75 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6537 (mp)
REVERT: B  289 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6770 (t70)
REVERT: B  312 TRP cc_start: 0.8689 (p-90) cc_final: 0.8316 (p-90)
REVERT: B  404 LYS cc_start: 0.8684 (tppt) cc_final: 0.8406 (mmmm)
  outliers start: 40
  outliers final: 26
  residues processed: 148
  average time/residue: 0.1423
  time to fit residues: 27.5983
Evaluate side-chains
  155 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
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   51 LEU
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  264 VAL
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   90 THR
Chi-restraints excluded: chain B residue  110 MET
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  405 ASP
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:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 30 optimal weight:    0.2980
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 ASN
B 127 ASN
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.215127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.157873 restraints weight = 5175.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.162238 restraints weight = 3667.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.165309 restraints weight = 2995.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.4321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.223   4869  Z= 0.187
  Angle     :  0.617   8.131   6614  Z= 0.326
  Chirality :  0.043   0.136    799
  Planarity :  0.004   0.037    825
  Dihedral  :  4.547  34.310    658
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 23.64 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.33 %

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:  1.39 (0.35), residues: 614
  helix:  1.97 (0.25), residues: 418
  sheet: -1.66 (0.85), residues: 42
  loop : -1.24 (0.54), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 375 
 HIS   0.045   0.003   HIS A 148 
 PHE   0.011   0.001   PHE A 421 
 TYR   0.036   0.002   TYR A 396 
 ARG   0.002   0.000   ARG B  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04409 (  351)
  hydrogen bonds       : angle       4.62144 ( 1053)
  metal coordination   : bond        0.06898 (   14)
  SS BOND              : bond        0.00215 (    5)
  SS BOND              : angle       0.85571 (   10)
  covalent geometry    : bond        0.00307 ( 4850)
  covalent geometry    : angle       0.61630 ( 6604)

*********************** 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
  154 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6383 (mpp)
REVERT: A   62 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7755 (mtm-85)
REVERT: A   68 GLN cc_start: 0.7608 (tt0) cc_final: 0.7324 (tt0)
REVERT: A   75 ILE cc_start: 0.6481 (OUTLIER) cc_final: 0.5864 (mp)
REVERT: A   97 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7652 (tp)
REVERT: A  115 VAL cc_start: 0.8969 (m) cc_final: 0.8759 (p)
REVERT: A  312 TRP cc_start: 0.8596 (p-90) cc_final: 0.8247 (p-90)
REVERT: A  420 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7532 (tt0)
REVERT: B   42 PHE cc_start: 0.7785 (m-80) cc_final: 0.7450 (m-80)
REVERT: B   75 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6215 (mp)
REVERT: B  289 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6752 (t70)
REVERT: B  312 TRP cc_start: 0.8589 (p-90) cc_final: 0.7983 (p-90)
REVERT: B  404 LYS cc_start: 0.8599 (tppt) cc_final: 0.8320 (mmmm)
  outliers start: 26
  outliers final: 14
  residues processed: 138
  average time/residue: 0.1452
  time to fit residues: 26.4039
Evaluate side-chains
  135 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
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   97 LEU
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   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  289 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    0.4980
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4399 r_free = 0.4399 target = 0.213229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.155744 restraints weight = 5229.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.160110 restraints weight = 3697.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.162999 restraints weight = 3012.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   4869  Z= 0.166
  Angle     :  0.632   8.803   6614  Z= 0.330
  Chirality :  0.044   0.175    799
  Planarity :  0.004   0.031    825
  Dihedral  :  4.412  28.913    658
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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:  1.36 (0.35), residues: 614
  helix:  1.91 (0.24), residues: 418
  sheet: -1.56 (0.91), residues: 38
  loop : -1.21 (0.52), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 375 
 HIS   0.035   0.003   HIS A 148 
 PHE   0.008   0.001   PHE A 421 
 TYR   0.026   0.002   TYR A 396 
 ARG   0.002   0.000   ARG B  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04466 (  351)
  hydrogen bonds       : angle       4.56060 ( 1053)
  metal coordination   : bond        0.03421 (   14)
  SS BOND              : bond        0.00275 (    5)
  SS BOND              : angle       0.78419 (   10)
  covalent geometry    : bond        0.00364 ( 4850)
  covalent geometry    : angle       0.63181 ( 6604)

*********************** 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
  147 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6349 (mpp)
REVERT: A   62 ARG cc_start: 0.8080 (mmt180) cc_final: 0.7792 (mtm-85)
REVERT: A   68 GLN cc_start: 0.7480 (tt0) cc_final: 0.7196 (tt0)
REVERT: A   75 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6162 (mp)
REVERT: A   97 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7670 (tp)
REVERT: A  115 VAL cc_start: 0.8998 (m) cc_final: 0.8773 (p)
REVERT: A  312 TRP cc_start: 0.8673 (p-90) cc_final: 0.8359 (p-90)
REVERT: A  420 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7449 (tt0)
REVERT: B   42 PHE cc_start: 0.7744 (m-80) cc_final: 0.7412 (m-80)
REVERT: B   75 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6269 (mp)
REVERT: B  289 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6745 (t70)
REVERT: B  312 TRP cc_start: 0.8676 (p-90) cc_final: 0.8343 (p-90)
REVERT: B  404 LYS cc_start: 0.8577 (tppt) cc_final: 0.8321 (mmmm)
  outliers start: 23
  outliers final: 13
  residues processed: 135
  average time/residue: 0.1492
  time to fit residues: 25.8689
Evaluate side-chains
  135 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
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   97 LEU
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   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  289 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0010
   chunk 18 optimal weight:   50.0000
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.5186

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.215997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.158764 restraints weight = 5232.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.163190 restraints weight = 3732.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.166163 restraints weight = 3042.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.4594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4869  Z= 0.149
  Angle     :  0.614   8.932   6614  Z= 0.324
  Chirality :  0.043   0.147    799
  Planarity :  0.004   0.030    825
  Dihedral  :  4.475  35.677    658
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 25.25 %
    Favored  : 70.91 %
  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:  1.30 (0.35), residues: 614
  helix:  1.91 (0.24), residues: 418
  sheet: -1.82 (0.86), residues: 42
  loop : -1.27 (0.52), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 375 
 HIS   0.012   0.002   HIS B 148 
 PHE   0.009   0.001   PHE A 421 
 TYR   0.018   0.001   TYR A 396 
 ARG   0.006   0.000   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04357 (  351)
  hydrogen bonds       : angle       4.53575 ( 1053)
  metal coordination   : bond        0.02596 (   14)
  SS BOND              : bond        0.00195 (    5)
  SS BOND              : angle       0.58794 (   10)
  covalent geometry    : bond        0.00322 ( 4850)
  covalent geometry    : angle       0.61452 ( 6604)

********************** 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: 19
    poor density    : 120
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.7434 (tt0) cc_final: 0.7064 (tt0)
REVERT: A   75 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.5950 (mp)
REVERT: A   97 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7676 (tp)
REVERT: A  312 TRP cc_start: 0.8725 (p-90) cc_final: 0.8429 (p-90)
REVERT: A  420 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7480 (tt0)
REVERT: B   75 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6060 (mp)
REVERT: B  312 TRP cc_start: 0.8774 (p-90) cc_final: 0.8449 (p-90)
REVERT: B  354 ARG cc_start: 0.7921 (mpp80) cc_final: 0.7457 (mpp80)
REVERT: B  404 LYS cc_start: 0.8567 (tppt) cc_final: 0.8334 (mmmm)
  outliers start: 19
  outliers final: 14
  residues processed: 127
  average time/residue: 0.1444
  time to fit residues: 23.9700
Evaluate side-chains
  138 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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   97 LEU
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   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  385 THR
Chi-restraints excluded: chain B residue  415 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 46 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 43 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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 HIS
** 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 = 0.4411 r_free = 0.4411 target = 0.214050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.157367 restraints weight = 5322.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.161499 restraints weight = 3809.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.164513 restraints weight = 3113.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.4721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.472   4869  Z= 0.277
  Angle     :  0.624   8.899   6614  Z= 0.329
  Chirality :  0.043   0.159    799
  Planarity :  0.004   0.025    825
  Dihedral  :  4.427  28.623    658
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 26.26 %
    Favored  : 69.70 %
  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:  1.23 (0.34), residues: 614
  helix:  1.87 (0.24), residues: 418
  sheet: -1.88 (0.86), residues: 42
  loop : -1.33 (0.52), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 375 
 HIS   0.015   0.002   HIS A 148 
 PHE   0.008   0.001   PHE B  94 
 TYR   0.019   0.001   TYR B 396 
 ARG   0.006   0.000   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04416 (  351)
  hydrogen bonds       : angle       4.50582 ( 1053)
  metal coordination   : bond        0.12899 (   14)
  SS BOND              : bond        0.00209 (    5)
  SS BOND              : angle       0.56965 (   10)
  covalent geometry    : bond        0.00363 ( 4850)
  covalent geometry    : angle       0.62455 ( 6604)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1826.62 seconds
wall clock time: 32 minutes 18.99 seconds (1938.99 seconds total)