Starting phenix.real_space_refine
on Tue Feb 11 09:58:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8csw_26973/02_2025/8csw_26973.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8csw_26973/02_2025/8csw_26973.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8csw_26973/02_2025/8csw_26973.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8csw_26973/02_2025/8csw_26973.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8csw_26973/02_2025/8csw_26973.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8csw_26973/02_2025/8csw_26973.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.272
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    3278      2.51       5
     N     915      2.21       5
     O    1116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5332
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "X"
      Number of atoms: 5167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 657, 5167
          Classifications: {'peptide': 657}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 30, 'TRANS': 626}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "X"
      Number of atoms: 165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 165
          Classifications: {'water': 165}
          Link IDs: {None: 164}
  Time building chain proxies: 4.18, per 1000 atoms: 0.78
  Number of scatterers: 5332
  At special positions: 0
  Unit cell: (95.45, 102.92, 71.795, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O    1116      8.00
     N     915      7.00
     C    3278      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.30
  Conformation dependent library (CDL) restraints added in 605.5 milliseconds
  

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1232

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 10 sheets defined
      21.2% alpha, 41.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'X' and resid 13 through 21
    Processing helix  chain 'X' and resid 51 through 58
      removed outlier: 3.658A  pdb=" N   ALA X  55 " --> pdb=" O   ALA X  51 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 151 through 159
    Processing helix  chain 'X' and resid 187 through 197
    Processing helix  chain 'X' and resid 201 through 206
      removed outlier: 3.998A  pdb=" N   SER X 206 " --> pdb=" O   GLU X 203 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 207 through 227
    Processing helix  chain 'X' and resid 247 through 258
      removed outlier: 4.118A  pdb=" N   ILE X 251 " --> pdb=" O   GLY X 247 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 264 through 268
    Processing helix  chain 'X' and resid 269 through 283
      removed outlier: 4.363A  pdb=" N   ALA X 273 " --> pdb=" O   TRP X 269 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 368 through 373
    Processing helix  chain 'X' and resid 381 through 389
      removed outlier: 3.745A  pdb=" N   ILE X 389 " --> pdb=" O   LEU X 385 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 431 through 436
      removed outlier: 3.869A  pdb=" N   TYR X 435 " --> pdb=" O   ILE X 431 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 441 through 459
    Processing helix  chain 'X' and resid 550 through 552
      No H-bonds generated for 'chain 'X' and resid 550 through 552'
    Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11
      removed outlier: 3.509A  pdb=" N   GLU X  96 " --> pdb=" O   THR X 103 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   SER X 105 " --> pdb=" O   VAL X  94 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   VAL X  94 " --> pdb=" O   SER X 105 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   THR X 107 " --> pdb=" O   ALA X  92 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   ALA X  92 " --> pdb=" O   THR X 107 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'X' and resid 31 through 34
      removed outlier: 4.693A  pdb=" N   LEU X  31 " --> pdb=" O   GLN X 133 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   LEU X 130 " --> pdb=" O   LEU X 121 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   LEU X 121 " --> pdb=" O   LEU X 130 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY X 132 " --> pdb=" O   LEU X 119 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 169
    Processing sheet with id=AA4, first strand: chain 'X' and resid 322 through 327
      removed outlier: 6.303A  pdb=" N   PHE X 326 " --> pdb=" O   PHE X 292 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   PHE X 292 " --> pdb=" O   PHE X 326 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   THR X 330 " --> pdb=" O   LEU X 349 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   SER X 362 " --> pdb=" O   SER X 352 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'X' and resid 322 through 327
      removed outlier: 6.303A  pdb=" N   PHE X 326 " --> pdb=" O   PHE X 292 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   PHE X 292 " --> pdb=" O   PHE X 326 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   VAL X 288 " --> pdb=" O   LYS X 421 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   LYS X 421 " --> pdb=" O   VAL X 288 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   PHE X 292 " --> pdb=" O   ASN X 417 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   ASN X 417 " --> pdb=" O   PHE X 292 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'X' and resid 303 through 308
      removed outlier: 6.068A  pdb=" N   ILE X 304 " --> pdb=" O   VAL X 394 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   TRP X 396 " --> pdb=" O   ILE X 304 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   GLU X 306 " --> pdb=" O   TRP X 396 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   CYS X 398 " --> pdb=" O   GLU X 306 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   TYR X 308 " --> pdb=" O   CYS X 398 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   CYS X 393 " --> pdb=" O   SER X 409 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   SER X 409 " --> pdb=" O   CYS X 393 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   VAL X 395 " --> pdb=" O   THR X 407 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   SER X 576 " --> pdb=" O   LEU X 406 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   LEU X 485 " --> pdb=" O   CYS X 586 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'X' and resid 303 through 308
      removed outlier: 6.068A  pdb=" N   ILE X 304 " --> pdb=" O   VAL X 394 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   TRP X 396 " --> pdb=" O   ILE X 304 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   GLU X 306 " --> pdb=" O   TRP X 396 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   CYS X 398 " --> pdb=" O   GLU X 306 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   TYR X 308 " --> pdb=" O   CYS X 398 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   CYS X 393 " --> pdb=" O   SER X 409 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   SER X 409 " --> pdb=" O   CYS X 393 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   VAL X 395 " --> pdb=" O   THR X 407 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   SER X 576 " --> pdb=" O   LEU X 406 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LYS X 505 " --> pdb=" O   LEU X 533 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU X 533 " --> pdb=" O   LYS X 505 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   VAL X 507 " --> pdb=" O   LEU X 531 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LEU X 531 " --> pdb=" O   VAL X 507 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   LEU X 509 " --> pdb=" O   LYS X 529 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   LYS X 529 " --> pdb=" O   LEU X 509 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   ILE X 511 " --> pdb=" O   TRP X 527 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   TRP X 527 " --> pdb=" O   ILE X 511 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   VAL X 513 " --> pdb=" O   LYS X 525 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   LYS X 525 " --> pdb=" O   VAL X 513 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ALA X 515 " --> pdb=" O   ALA X 523 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480
    Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593
    Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599
      removed outlier: 6.536A  pdb=" N   ALA X 598 " --> pdb=" O   VAL X 685 " (cutoff:3.500A)

    214 hydrogen bonds defined for protein.
    600 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: 2.16

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 899
        1.32 -     1.44: 1339
        1.44 -     1.57: 3004
        1.57 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 5273
  Sorted by residual:
  bond pdb=" N   TRP X  89 "
       pdb=" CA  TRP X  89 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.040 1.17e-02 7.31e+03 1.14e+01
  bond pdb=" N   GLU X 405 "
       pdb=" CA  GLU X 405 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.039 1.21e-02 6.83e+03 1.06e+01
  bond pdb=" N   ILE X 104 "
       pdb=" CA  ILE X 104 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.20e-02 6.94e+03 1.01e+01
  bond pdb=" CA  SER X 105 "
       pdb=" CB  SER X 105 "
    ideal  model  delta    sigma   weight residual
    1.529  1.485  0.044 1.43e-02 4.89e+03 9.52e+00
  bond pdb=" N   VAL X 211 "
       pdb=" CA  VAL X 211 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.19e-02 7.06e+03 9.17e+00
  ... (remaining 5268 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 6768
        1.78 -     3.56: 322
        3.56 -     5.33: 50
        5.33 -     7.11: 11
        7.11 -     8.89: 2
  Bond angle restraints: 7153
  Sorted by residual:
  angle pdb=" N   ASP X 408 "
        pdb=" CA  ASP X 408 "
        pdb=" C   ASP X 408 "
      ideal   model   delta    sigma   weight residual
     109.96  101.96    8.00 1.50e+00 4.44e-01 2.85e+01
  angle pdb=" C   THR X 403 "
        pdb=" N   LEU X 404 "
        pdb=" CA  LEU X 404 "
      ideal   model   delta    sigma   weight residual
     123.11  117.38    5.73 1.42e+00 4.96e-01 1.63e+01
  angle pdb=" C   GLY X  85 "
        pdb=" N   ASP X  86 "
        pdb=" CA  ASP X  86 "
      ideal   model   delta    sigma   weight residual
     121.99  116.05    5.94 1.49e+00 4.50e-01 1.59e+01
  angle pdb=" CA  LEU X 404 "
        pdb=" C   LEU X 404 "
        pdb=" O   LEU X 404 "
      ideal   model   delta    sigma   weight residual
     120.46  116.22    4.24 1.07e+00 8.73e-01 1.57e+01
  angle pdb=" CB  ARG X 287 "
        pdb=" CG  ARG X 287 "
        pdb=" CD  ARG X 287 "
      ideal   model   delta    sigma   weight residual
     111.30  102.41    8.89 2.30e+00 1.89e-01 1.49e+01
  ... (remaining 7148 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 2890
       17.21 -    34.42: 199
       34.42 -    51.63: 59
       51.63 -    68.84: 21
       68.84 -    86.04: 7
  Dihedral angle restraints: 3176
    sinusoidal: 1276
      harmonic: 1900
  Sorted by residual:
  dihedral pdb=" CA  GLU X 185 "
           pdb=" C   GLU X 185 "
           pdb=" N   GLY X 186 "
           pdb=" CA  GLY X 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.57  -20.43     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  ILE X 418 "
           pdb=" C   ILE X 418 "
           pdb=" N   SER X 419 "
           pdb=" CA  SER X 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.11  -16.89     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" C   ILE X 431 "
           pdb=" N   ILE X 431 "
           pdb=" CA  ILE X 431 "
           pdb=" CB  ILE X 431 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -129.86    7.86     0      2.50e+00 1.60e-01 9.88e+00
  ... (remaining 3173 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 577
       0.050 -    0.100: 168
       0.100 -    0.150: 39
       0.150 -    0.199: 17
       0.199 -    0.249: 8
  Chirality restraints: 809
  Sorted by residual:
  chirality pdb=" CB  VAL X 106 "
            pdb=" CA  VAL X 106 "
            pdb=" CG1 VAL X 106 "
            pdb=" CG2 VAL X 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  LEU X 349 "
            pdb=" N   LEU X 349 "
            pdb=" C   LEU X 349 "
            pdb=" CB  LEU X 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  SER X 329 "
            pdb=" N   SER X 329 "
            pdb=" C   SER X 329 "
            pdb=" CB  SER X 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 806 not shown)

  Planarity restraints: 921
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP X 364 "   -0.016 2.00e-02 2.50e+03   3.29e-02 1.08e+01
        pdb=" C   ASP X 364 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ASP X 364 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LEU X 365 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER X 576 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.21e+00
        pdb=" C   SER X 576 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   SER X 576 "    0.020 2.00e-02 2.50e+03
        pdb=" N   CYS X 577 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP X  89 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.03e+00
        pdb=" C   TRP X  89 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   TRP X  89 "    0.017 2.00e-02 2.50e+03
        pdb=" N   TRP X  90 "    0.016 2.00e-02 2.50e+03
  ... (remaining 918 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 691
        2.76 -     3.29: 4879
        3.29 -     3.83: 9713
        3.83 -     4.36: 11710
        4.36 -     4.90: 19288
  Nonbonded interactions: 46281
  Sorted by model distance:
  nonbonded pdb=" O   HOH X 738 "
            pdb=" O   HOH X 851 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   HOH X 768 "
            pdb=" O   HOH X 798 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   HOH X 792 "
            pdb=" O   HOH X 838 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   HOH X 755 "
            pdb=" O   HOH X 839 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   ASP X 426 "
            pdb=" O   HOH X 701 "
     model   vdw
     2.283 3.040
  ... (remaining 46276 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.410
  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:          0.490
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.790
  Find NCS groups from input model:        0.080
  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:15.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
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      :  0.007   0.047   5273  Z= 0.429
  Angle     :  0.862   8.892   7153  Z= 0.555
  Chirality :  0.057   0.249    809
  Planarity :  0.006   0.038    921
  Dihedral  : 14.462  86.044   1944
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  8.24 %
    Favored  : 89.43 %
  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:  0.83 (0.31), residues: 647
  helix:  0.80 (0.45), residues: 116
  sheet:  0.87 (0.31), residues: 250
  loop :  0.30 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP X  90 
 HIS   0.005   0.001   HIS X 632 
 PHE   0.022   0.002   PHE X 639 
 TYR   0.017   0.002   TYR X 167 
 ARG   0.003   0.001   ARG X 450 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.596 
Fit side-chains
REVERT: X   16 ARG cc_start: 0.7419 (ttm170) cc_final: 0.7217 (tmm-80)
REVERT: X   88 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7557 (mmpt)
REVERT: X  143 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7961 (ttm-80)
REVERT: X  194 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7695 (ttp-110)
REVERT: X  442 LEU cc_start: 0.8074 (mp) cc_final: 0.7733 (mm)
REVERT: X  445 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7647 (ttpp)
REVERT: X  446 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: X  452 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6893 (mt-10)
REVERT: X  483 SER cc_start: 0.8344 (p) cc_final: 0.8047 (m)
REVERT: X  508 GLN cc_start: 0.7339 (tt0) cc_final: 0.6839 (mt0)
REVERT: X  593 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8154 (tppt)
REVERT: X  638 ARG cc_start: 0.7856 (mpt90) cc_final: 0.6170 (mtm110)
REVERT: X  647 THR cc_start: 0.8417 (m) cc_final: 0.8179 (p)
REVERT: X  651 LYS cc_start: 0.7522 (mptt) cc_final: 0.7244 (pttp)
  outliers start: 13
  outliers final: 6
  residues processed: 130
  average time/residue: 1.5292
  time to fit residues: 206.2635
Evaluate side-chains
  111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  404 LEU
Chi-restraints excluded: chain X residue  406 LEU
Chi-restraints excluded: chain X residue  549 PHE
Chi-restraints excluded: chain X residue  576 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
X  64 GLN
X  76 GLN
X 133 GLN
X 154 GLN
X 314 GLN
X 433 GLN
X 559 ASN
X 570 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.128562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.103948 restraints weight = 4985.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.25
r_work: 0.2920 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5273  Z= 0.143
  Angle     :  0.493   5.409   7153  Z= 0.258
  Chirality :  0.041   0.145    809
  Planarity :  0.004   0.041    921
  Dihedral  :  6.191  58.775    719
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 11.47 %
    Favored  : 85.84 %
  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:  1.12 (0.31), residues: 647
  helix:  1.80 (0.46), residues: 117
  sheet:  0.63 (0.31), residues: 246
  loop :  0.57 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP X  90 
 HIS   0.006   0.001   HIS X 570 
 PHE   0.010   0.001   PHE X 548 
 TYR   0.011   0.001   TYR X 167 
 ARG   0.008   0.000   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.639 
Fit side-chains
REVERT: X   16 ARG cc_start: 0.7615 (ttm170) cc_final: 0.7405 (tmm-80)
REVERT: X  127 LYS cc_start: 0.6397 (ttpp) cc_final: 0.5941 (ttpt)
REVERT: X  133 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7727 (mm110)
REVERT: X  143 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.7920 (ttm-80)
REVERT: X  194 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7735 (ttm110)
REVERT: X  442 LEU cc_start: 0.7947 (mp) cc_final: 0.7583 (mm)
REVERT: X  445 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7676 (ttpp)
REVERT: X  446 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7628 (tm-30)
REVERT: X  452 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6778 (mt-10)
REVERT: X  483 SER cc_start: 0.8238 (p) cc_final: 0.8022 (m)
REVERT: X  508 GLN cc_start: 0.7613 (tt0) cc_final: 0.6897 (mt0)
REVERT: X  593 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8246 (tppt)
REVERT: X  597 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7644 (mtmt)
REVERT: X  599 GLU cc_start: 0.8304 (tt0) cc_final: 0.7857 (tm-30)
REVERT: X  638 ARG cc_start: 0.7811 (mpt90) cc_final: 0.5916 (mtm110)
REVERT: X  647 THR cc_start: 0.8351 (m) cc_final: 0.8111 (p)
REVERT: X  651 LYS cc_start: 0.7421 (mptt) cc_final: 0.7011 (pttp)
  outliers start: 15
  outliers final: 5
  residues processed: 110
  average time/residue: 1.4538
  time to fit residues: 165.9097
Evaluate side-chains
  104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  133 GLN
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  570 HIS
Chi-restraints excluded: chain X residue  576 SER
Chi-restraints excluded: chain X residue  597 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
X 154 GLN
** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 570 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.128747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.104193 restraints weight = 5021.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.25
r_work: 0.2910 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5273  Z= 0.155
  Angle     :  0.492   5.491   7153  Z= 0.254
  Chirality :  0.041   0.138    809
  Planarity :  0.004   0.033    921
  Dihedral  :  4.822  46.093    713
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.19 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.32), residues: 647
  helix:  2.00 (0.47), residues: 117
  sheet:  0.56 (0.31), residues: 245
  loop :  0.64 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP X  90 
 HIS   0.002   0.001   HIS X  22 
 PHE   0.010   0.001   PHE X 639 
 TYR   0.012   0.001   TYR X 167 
 ARG   0.007   0.000   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.611 
Fit side-chains
REVERT: X   16 ARG cc_start: 0.7604 (ttm170) cc_final: 0.7400 (tmm-80)
REVERT: X  127 LYS cc_start: 0.6406 (ttpp) cc_final: 0.6023 (ttpt)
REVERT: X  143 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.7889 (ttm-80)
REVERT: X  442 LEU cc_start: 0.7950 (mp) cc_final: 0.7577 (mm)
REVERT: X  445 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7678 (ttpp)
REVERT: X  446 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7557 (tm-30)
REVERT: X  452 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6761 (mt-10)
REVERT: X  593 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8199 (ttmt)
REVERT: X  599 GLU cc_start: 0.8287 (tt0) cc_final: 0.7795 (tm-30)
REVERT: X  638 ARG cc_start: 0.7780 (mpt90) cc_final: 0.5869 (mtm110)
REVERT: X  651 LYS cc_start: 0.7423 (mptt) cc_final: 0.6877 (mmtp)
REVERT: X  672 MET cc_start: 0.8475 (mmp) cc_final: 0.8159 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 109
  average time/residue: 1.5000
  time to fit residues: 169.3212
Evaluate side-chains
  102 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  586 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0980
   chunk 32 optimal weight:    0.0370
   chunk 61 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.0262

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

Flipped N/Q/H residues before XYZ refinement:
** X 314 GLN ** 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 = 0.3353 r_free = 0.3353 target = 0.129788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.104882 restraints weight = 5144.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 1.28
r_work: 0.2915 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5273  Z= 0.134
  Angle     :  0.463   5.454   7153  Z= 0.239
  Chirality :  0.040   0.134    809
  Planarity :  0.004   0.036    921
  Dihedral  :  4.544  47.723    711
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.80 %
    Favored  : 84.59 %
  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:  1.21 (0.32), residues: 647
  helix:  2.15 (0.47), residues: 117
  sheet:  0.52 (0.31), residues: 248
  loop :  0.66 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP X  90 
 HIS   0.002   0.001   HIS X  22 
 PHE   0.010   0.001   PHE X 639 
 TYR   0.011   0.001   TYR X 167 
 ARG   0.006   0.000   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.593 
Fit side-chains
REVERT: X   16 ARG cc_start: 0.7622 (ttm170) cc_final: 0.7418 (tmm-80)
REVERT: X  127 LYS cc_start: 0.6428 (ttpp) cc_final: 0.6061 (ttpt)
REVERT: X  143 ARG cc_start: 0.8495 (ttp-170) cc_final: 0.7897 (ttm-80)
REVERT: X  405 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6552 (tp30)
REVERT: X  442 LEU cc_start: 0.7940 (mp) cc_final: 0.7537 (mm)
REVERT: X  445 LYS cc_start: 0.8207 (tmtt) cc_final: 0.7606 (ttpp)
REVERT: X  446 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7386 (tm-30)
REVERT: X  452 GLU cc_start: 0.7599 (mm-30) cc_final: 0.6742 (mt-10)
REVERT: X  597 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7668 (mtmt)
REVERT: X  599 GLU cc_start: 0.8260 (tt0) cc_final: 0.7793 (tm-30)
REVERT: X  638 ARG cc_start: 0.7758 (mpt90) cc_final: 0.5815 (mtm110)
REVERT: X  651 LYS cc_start: 0.7401 (mptt) cc_final: 0.6859 (mmtp)
  outliers start: 9
  outliers final: 4
  residues processed: 111
  average time/residue: 1.5897
  time to fit residues: 182.3644
Evaluate side-chains
  107 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  177 GLU
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  586 CYS
Chi-restraints excluded: chain X residue  597 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
X 122 GLN
X 133 GLN
** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 508 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.128767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.103908 restraints weight = 4976.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.26
r_work: 0.2907 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5273  Z= 0.157
  Angle     :  0.480   5.496   7153  Z= 0.246
  Chirality :  0.040   0.135    809
  Planarity :  0.004   0.036    921
  Dihedral  :  4.626  48.375    711
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.80 %
    Favored  : 83.51 %
  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:  1.19 (0.32), residues: 647
  helix:  2.11 (0.47), residues: 117
  sheet:  0.50 (0.31), residues: 243
  loop :  0.68 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X  90 
 HIS   0.003   0.001   HIS X  22 
 PHE   0.008   0.001   PHE X 639 
 TYR   0.012   0.001   TYR X 167 
 ARG   0.008   0.000   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.577 
Fit side-chains
REVERT: X  127 LYS cc_start: 0.6433 (ttpp) cc_final: 0.6078 (ttpt)
REVERT: X  133 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7810 (mm110)
REVERT: X  143 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.7895 (ttm-80)
REVERT: X  310 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7076 (mp0)
REVERT: X  405 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6671 (tp30)
REVERT: X  442 LEU cc_start: 0.7960 (mp) cc_final: 0.7557 (mm)
REVERT: X  445 LYS cc_start: 0.8207 (tmtt) cc_final: 0.7607 (ttpp)
REVERT: X  446 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: X  452 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6752 (mt-10)
REVERT: X  533 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7146 (mt)
REVERT: X  593 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8032 (mttp)
REVERT: X  599 GLU cc_start: 0.8265 (tt0) cc_final: 0.7790 (tm-30)
REVERT: X  638 ARG cc_start: 0.7765 (mpt90) cc_final: 0.5815 (mtm110)
REVERT: X  651 LYS cc_start: 0.7411 (mptt) cc_final: 0.6874 (mmtp)
REVERT: X  672 MET cc_start: 0.8491 (mmp) cc_final: 0.8189 (mmm)
  outliers start: 15
  outliers final: 6
  residues processed: 113
  average time/residue: 1.5047
  time to fit residues: 176.1371
Evaluate side-chains
  112 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  133 GLN
Chi-restraints excluded: chain X residue  177 GLU
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  533 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  581 GLU
Chi-restraints excluded: chain X residue  586 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0040
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.5598

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

Flipped N/Q/H residues before XYZ refinement:
** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 508 GLN ** 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 = 0.3337 r_free = 0.3337 target = 0.128491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.104170 restraints weight = 5023.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.23
r_work: 0.2908 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5273  Z= 0.165
  Angle     :  0.485   5.503   7153  Z= 0.248
  Chirality :  0.041   0.137    809
  Planarity :  0.004   0.038    921
  Dihedral  :  4.669  48.787    711
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.05 %
    Favored  : 83.15 %
  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:  1.20 (0.32), residues: 647
  helix:  2.15 (0.47), residues: 116
  sheet:  0.49 (0.32), residues: 244
  loop :  0.67 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP X  90 
 HIS   0.003   0.001   HIS X  22 
 PHE   0.008   0.001   PHE X  39 
 TYR   0.013   0.001   TYR X 167 
 ARG   0.010   0.000   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.650 
Fit side-chains
REVERT: X  127 LYS cc_start: 0.6479 (ttpp) cc_final: 0.6104 (ttpt)
REVERT: X  143 ARG cc_start: 0.8471 (ttp-170) cc_final: 0.7892 (ttm-80)
REVERT: X  310 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7081 (mp0)
REVERT: X  405 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6664 (tp30)
REVERT: X  442 LEU cc_start: 0.7967 (mp) cc_final: 0.7584 (mm)
REVERT: X  445 LYS cc_start: 0.8205 (tmtt) cc_final: 0.7610 (ttpp)
REVERT: X  446 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7496 (tm-30)
REVERT: X  452 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6749 (mt-10)
REVERT: X  593 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8038 (mttp)
REVERT: X  599 GLU cc_start: 0.8250 (tt0) cc_final: 0.7775 (tm-30)
REVERT: X  638 ARG cc_start: 0.7755 (mpt90) cc_final: 0.5803 (mtm110)
REVERT: X  651 LYS cc_start: 0.7421 (mptt) cc_final: 0.6876 (mmtp)
  outliers start: 10
  outliers final: 6
  residues processed: 110
  average time/residue: 1.4632
  time to fit residues: 166.7808
Evaluate side-chains
  110 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  177 GLU
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  581 GLU
Chi-restraints excluded: chain X residue  586 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 35 optimal weight:    0.0040
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.7396

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

Flipped N/Q/H residues before XYZ refinement:
** X 508 GLN ** 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 = 0.3332 r_free = 0.3332 target = 0.128090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.103193 restraints weight = 4964.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.25
r_work: 0.2893 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5273  Z= 0.177
  Angle     :  0.497   5.597   7153  Z= 0.254
  Chirality :  0.041   0.138    809
  Planarity :  0.004   0.040    921
  Dihedral  :  4.734  48.910    711
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.87 %
    Favored  : 82.80 %
  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:  1.15 (0.32), residues: 647
  helix:  2.10 (0.47), residues: 116
  sheet:  0.48 (0.32), residues: 244
  loop :  0.64 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X  90 
 HIS   0.003   0.001   HIS X  22 
 PHE   0.008   0.001   PHE X 639 
 TYR   0.013   0.001   TYR X 167 
 ARG   0.010   0.000   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.569 
Fit side-chains
REVERT: X   96 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7309 (tm-30)
REVERT: X  127 LYS cc_start: 0.6453 (ttpp) cc_final: 0.6073 (ttpt)
REVERT: X  143 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.7901 (ttm-80)
REVERT: X  213 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7923 (mtt180)
REVERT: X  310 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7068 (mp0)
REVERT: X  405 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6658 (tp30)
REVERT: X  442 LEU cc_start: 0.7964 (mp) cc_final: 0.7575 (mm)
REVERT: X  445 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7600 (ttpp)
REVERT: X  446 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7427 (tm-30)
REVERT: X  452 GLU cc_start: 0.7619 (mm-30) cc_final: 0.6732 (mt-10)
REVERT: X  593 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8045 (mttp)
REVERT: X  599 GLU cc_start: 0.8271 (tt0) cc_final: 0.7789 (tm-30)
REVERT: X  638 ARG cc_start: 0.7767 (mpt90) cc_final: 0.5832 (mtm110)
REVERT: X  651 LYS cc_start: 0.7447 (mptt) cc_final: 0.6900 (mmtp)
REVERT: X  672 MET cc_start: 0.8518 (mmp) cc_final: 0.8243 (mmm)
  outliers start: 13
  outliers final: 7
  residues processed: 112
  average time/residue: 1.5479
  time to fit residues: 179.2491
Evaluate side-chains
  113 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   96 GLU
Chi-restraints excluded: chain X residue  177 GLU
Chi-restraints excluded: chain X residue  213 ARG
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  581 GLU
Chi-restraints excluded: chain X residue  586 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 10 optimal weight:    0.0980
   chunk 44 optimal weight:    2.9990
   overall best weight:    3.0188

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

Flipped N/Q/H residues before XYZ refinement:
** X 508 GLN ** 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 = 0.3307 r_free = 0.3307 target = 0.126210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.101329 restraints weight = 4981.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.26
r_work: 0.2864 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5273  Z= 0.264
  Angle     :  0.554   5.642   7153  Z= 0.285
  Chirality :  0.043   0.144    809
  Planarity :  0.004   0.042    921
  Dihedral  :  5.031  46.545    711
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.70 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.32), residues: 647
  helix:  1.85 (0.46), residues: 116
  sheet:  0.39 (0.31), residues: 249
  loop :  0.50 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP X  90 
 HIS   0.004   0.001   HIS X  22 
 PHE   0.011   0.002   PHE X 639 
 TYR   0.016   0.002   TYR X 167 
 ARG   0.011   0.001   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.609 
Fit side-chains
REVERT: X   96 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7342 (tm-30)
REVERT: X  133 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7819 (mm110)
REVERT: X  143 ARG cc_start: 0.8509 (ttp-170) cc_final: 0.7910 (ttm-80)
REVERT: X  213 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7964 (mtt180)
REVERT: X  405 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6534 (tp30)
REVERT: X  439 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7255 (mp0)
REVERT: X  442 LEU cc_start: 0.7996 (mp) cc_final: 0.7597 (mm)
REVERT: X  445 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7714 (ttpp)
REVERT: X  446 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7442 (tm-30)
REVERT: X  452 GLU cc_start: 0.7675 (mm-30) cc_final: 0.6764 (mt-10)
REVERT: X  593 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8171 (ttmt)
REVERT: X  599 GLU cc_start: 0.8277 (tt0) cc_final: 0.7762 (tm-30)
REVERT: X  638 ARG cc_start: 0.7837 (mpt90) cc_final: 0.5862 (mtm110)
REVERT: X  651 LYS cc_start: 0.7523 (mptt) cc_final: 0.6966 (mmtp)
  outliers start: 14
  outliers final: 9
  residues processed: 113
  average time/residue: 1.6097
  time to fit residues: 188.3724
Evaluate side-chains
  112 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   83 SER
Chi-restraints excluded: chain X residue   96 GLU
Chi-restraints excluded: chain X residue  133 GLN
Chi-restraints excluded: chain X residue  177 GLU
Chi-restraints excluded: chain X residue  213 ARG
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  439 GLU
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  581 GLU
Chi-restraints excluded: chain X residue  586 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0770
   chunk 32 optimal weight:    0.5980
   chunk 22 optimal weight:    0.4980
   overall best weight:    1.2342

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

Flipped N/Q/H residues before XYZ refinement:
** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 658 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.128502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.103895 restraints weight = 4970.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.25
r_work: 0.2903 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5273  Z= 0.154
  Angle     :  0.492   6.892   7153  Z= 0.252
  Chirality :  0.041   0.137    809
  Planarity :  0.004   0.045    921
  Dihedral  :  4.722  48.998    711
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.05 %
    Favored  : 82.62 %
  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:  1.09 (0.32), residues: 647
  helix:  2.03 (0.47), residues: 117
  sheet:  0.41 (0.31), residues: 243
  loop :  0.63 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP X  90 
 HIS   0.003   0.001   HIS X 658 
 PHE   0.008   0.001   PHE X 548 
 TYR   0.012   0.001   TYR X 167 
 ARG   0.010   0.000   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.640 
Fit side-chains
REVERT: X   96 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7283 (tm-30)
REVERT: X  127 LYS cc_start: 0.6395 (ttpp) cc_final: 0.5932 (ttpt)
REVERT: X  133 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7778 (mm110)
REVERT: X  143 ARG cc_start: 0.8488 (ttp-170) cc_final: 0.7907 (ttm-80)
REVERT: X  213 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7898 (mtt180)
REVERT: X  310 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7055 (mp0)
REVERT: X  405 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6493 (tp30)
REVERT: X  439 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7197 (mp0)
REVERT: X  442 LEU cc_start: 0.7963 (mp) cc_final: 0.7560 (mm)
REVERT: X  445 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7633 (ttpp)
REVERT: X  446 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7418 (tm-30)
REVERT: X  452 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6714 (mt-10)
REVERT: X  593 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8060 (mttp)
REVERT: X  599 GLU cc_start: 0.8250 (tt0) cc_final: 0.7772 (tm-30)
REVERT: X  638 ARG cc_start: 0.7785 (mpt90) cc_final: 0.5853 (mtm110)
REVERT: X  651 LYS cc_start: 0.7451 (mptt) cc_final: 0.6903 (mmtp)
REVERT: X  672 MET cc_start: 0.8524 (mmp) cc_final: 0.8308 (mmm)
  outliers start: 13
  outliers final: 6
  residues processed: 110
  average time/residue: 1.5490
  time to fit residues: 176.1494
Evaluate side-chains
  112 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   96 GLU
Chi-restraints excluded: chain X residue  133 GLN
Chi-restraints excluded: chain X residue  177 GLU
Chi-restraints excluded: chain X residue  213 ARG
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  439 GLU
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  586 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 28 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 658 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 = 0.3295 r_free = 0.3295 target = 0.125208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.100815 restraints weight = 5060.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.22
r_work: 0.2853 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5273  Z= 0.329
  Angle     :  0.603   5.950   7153  Z= 0.310
  Chirality :  0.044   0.149    809
  Planarity :  0.005   0.046    921
  Dihedral  :  5.207  45.541    711
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.59 %
    Favored  : 82.44 %
  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:  0.86 (0.31), residues: 647
  helix:  1.82 (0.46), residues: 114
  sheet:  0.38 (0.31), residues: 246
  loop :  0.39 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP X 205 
 HIS   0.005   0.002   HIS X 658 
 PHE   0.024   0.002   PHE X 548 
 TYR   0.018   0.002   TYR X 167 
 ARG   0.013   0.001   ARG X 259 

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

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

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1294 Ramachandran restraints generated.
    647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.601 
Fit side-chains
REVERT: X   96 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7332 (tm-30)
REVERT: X  127 LYS cc_start: 0.6446 (ttpp) cc_final: 0.5969 (ttpt)
REVERT: X  133 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7817 (mm110)
REVERT: X  143 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.7905 (ttm-80)
REVERT: X  194 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7687 (ttm110)
REVERT: X  213 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7994 (mtt180)
REVERT: X  405 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6649 (tp30)
REVERT: X  439 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7299 (mp0)
REVERT: X  442 LEU cc_start: 0.7997 (mp) cc_final: 0.7603 (mm)
REVERT: X  445 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7686 (ttpp)
REVERT: X  446 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7417 (tm-30)
REVERT: X  452 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6761 (mt-10)
REVERT: X  593 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8168 (ttmt)
REVERT: X  599 GLU cc_start: 0.8258 (tt0) cc_final: 0.7765 (tm-30)
REVERT: X  638 ARG cc_start: 0.7872 (mpt90) cc_final: 0.5901 (mtm110)
REVERT: X  651 LYS cc_start: 0.7546 (mptt) cc_final: 0.6985 (mmtp)
REVERT: X  672 MET cc_start: 0.8630 (mmp) cc_final: 0.8379 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 110
  average time/residue: 1.5522
  time to fit residues: 176.4709
Evaluate side-chains
  114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   96 GLU
Chi-restraints excluded: chain X residue  133 GLN
Chi-restraints excluded: chain X residue  177 GLU
Chi-restraints excluded: chain X residue  213 ARG
Chi-restraints excluded: chain X residue  281 CYS
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  439 GLU
Chi-restraints excluded: chain X residue  448 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  586 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
X 646 ASN
** X 658 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 = 0.3316 r_free = 0.3316 target = 0.126934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.101980 restraints weight = 5033.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 1.26
r_work: 0.2869 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5273  Z= 0.236
  Angle     :  0.549   6.276   7153  Z= 0.282
  Chirality :  0.042   0.144    809
  Planarity :  0.004   0.046    921
  Dihedral  :  5.061  46.506    711
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.41 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.32), residues: 647
  helix:  1.81 (0.46), residues: 116
  sheet:  0.38 (0.31), residues: 246
  loop :  0.41 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X  90 
 HIS   0.005   0.001   HIS X 658 
 PHE   0.010   0.002   PHE X  39 
 TYR   0.015   0.002   TYR X 167 
 ARG   0.012   0.001   ARG X 259 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5905.91 seconds
wall clock time: 104 minutes 44.43 seconds (6284.43 seconds total)