Starting phenix.real_space_refine
on Thu Feb 13 18:09:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hv8_0287/02_2025/6hv8_0287.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hv8_0287/02_2025/6hv8_0287.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hv8_0287/02_2025/6hv8_0287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hv8_0287/02_2025/6hv8_0287.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hv8_0287/02_2025/6hv8_0287.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hv8_0287/02_2025/6hv8_0287.cif"
  }
  resolution = 4.4
  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=   0.012
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      2      6.06       5
     S      47      5.16       5
     C    5904      2.51       5
     N    1546      2.21       5
     O    1707      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9206
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 3256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3256
          Classifications: {'peptide': 410}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 385}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "A"
      Number of atoms: 5948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 774, 5948
          Classifications: {'peptide': 774}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 92}
          Link IDs: {'CIS': 4, 'PTRANS': 28, 'TRANS': 741}
          Chain breaks: 9
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 379
          Unresolved non-hydrogen angles: 471
          Unresolved non-hydrogen dihedrals: 330
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 224
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8329  SG  CYS A2108      47.570  64.393  68.209  1.00113.75           S
  ATOM   8356  SG  CYS A2111      49.383  63.715  69.708  1.00115.28           S
  ATOM   8465  SG  CYS A2130      47.298  62.494  71.544  1.00102.72           S
  ATOM   8489  SG  CYS A2133      47.478  66.426  71.323  1.00106.59           S
  ATOM   8752  SG  CYS A2164      45.718  16.530  52.451  1.00196.52           S
  ATOM   8775  SG  CYS A2167      48.593  16.597  50.823  1.00212.37           S
  ATOM   8876  SG  CYS A2179      47.763  15.465  49.902  1.00190.38           S
  ATOM   8889  SG  CYS A2181      48.054  13.753  50.603  1.00197.38           S

  Time building chain proxies: 5.23, per 1000 atoms: 0.57
  Number of scatterers: 9206
  At special positions: 0
  Unit cell: (90.47, 112.27, 117.72, 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      2     29.99
     S      47     16.00
     O    1707      8.00
     N    1546      7.00
     C    5904      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: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2301 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A2108 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A2111 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A2133 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A2130 "
      pdb="  ZN A2302 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A2181 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A2164 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A2167 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A2179 "
      Number of angles added : 12


  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2280

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      33.9% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'B' and resid 210 through 232
      removed outlier: 3.573A  pdb=" N   LYS B 214 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   PHE B 218 " --> pdb=" O   LYS B 214 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ASN B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 276
      removed outlier: 3.658A  pdb=" N   LEU B 274 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 358
    Processing helix  chain 'B' and resid 384 through 394
      removed outlier: 4.201A  pdb=" N   HIS B 388 " --> pdb=" O   LYS B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 427
      removed outlier: 4.116A  pdb=" N   ASP B 426 " --> pdb=" O   GLN B 422 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ASP B 427 " --> pdb=" O   LYS B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 471
    Processing helix  chain 'B' and resid 509 through 512
    Processing helix  chain 'B' and resid 513 through 520
    Processing helix  chain 'B' and resid 546 through 551
      removed outlier: 3.920A  pdb=" N   LYS B 551 " --> pdb=" O   SER B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 610
    Processing helix  chain 'B' and resid 626 through 631
      removed outlier: 3.931A  pdb=" N   LEU B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1364 through 1369
    Processing helix  chain 'A' and resid 1532 through 1546
      removed outlier: 4.049A  pdb=" N   LYS A1538 " --> pdb=" O   GLN A1534 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   GLY A1541 " --> pdb=" O   GLU A1537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1567 through 1584
      removed outlier: 3.896A  pdb=" N   LEU A1573 " --> pdb=" O   LEU A1569 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A1580 " --> pdb=" O   GLU A1576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1597 through 1603
      removed outlier: 4.186A  pdb=" N   LEU A1601 " --> pdb=" O   ILE A1597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1626 through 1631
      removed outlier: 4.121A  pdb=" N   THR A1630 " --> pdb=" O   ASN A1626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1631 through 1636
    Processing helix  chain 'A' and resid 1636 through 1641
      removed outlier: 3.778A  pdb=" N   LEU A1640 " --> pdb=" O   VAL A1636 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER A1641 " --> pdb=" O   ASN A1637 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1636 through 1641'
    Processing helix  chain 'A' and resid 1641 through 1654
    Processing helix  chain 'A' and resid 1668 through 1678
      removed outlier: 3.570A  pdb=" N   ILE A1672 " --> pdb=" O   MET A1668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1738 through 1744
      removed outlier: 3.558A  pdb=" N   ASN A1742 " --> pdb=" O   ASN A1738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1787 through 1800
      removed outlier: 3.702A  pdb=" N   ASP A1800 " --> pdb=" O   LYS A1796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1807 through 1814
      removed outlier: 4.212A  pdb=" N   ASN A1814 " --> pdb=" O   ASP A1810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1815 through 1820
    Processing helix  chain 'A' and resid 1831 through 1852
      removed outlier: 3.849A  pdb=" N   HIS A1835 " --> pdb=" O   LEU A1831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1881 through 1892
      removed outlier: 3.500A  pdb=" N   MET A1885 " --> pdb=" O   TYR A1881 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG A1890 " --> pdb=" O   MET A1886 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR A1891 " --> pdb=" O   LYS A1887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1938 through 1943
    Processing helix  chain 'A' and resid 1949 through 1956
      removed outlier: 3.816A  pdb=" N   PHE A1953 " --> pdb=" O   TYR A1949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1957 through 1971
      removed outlier: 3.644A  pdb=" N   TYR A1971 " --> pdb=" O   THR A1967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1998 through 2003
    Processing helix  chain 'A' and resid 2005 through 2019
      Proline residue:  A2011  - end of helix
      removed outlier: 3.575A  pdb=" N   LYS A2014 " --> pdb=" O   LYS A2010 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2044 through 2058
      Proline residue:  A2050  - end of helix
    Processing helix  chain 'A' and resid 2067 through 2072
    Processing helix  chain 'A' and resid 2140 through 2158
    Processing helix  chain 'A' and resid 2190 through 2208
      removed outlier: 4.325A  pdb=" N   ILE A2194 " --> pdb=" O   PRO A2190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2210 through 2221
      removed outlier: 3.536A  pdb=" N   THR A2221 " --> pdb=" O   ILE A2217 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 171 through 173
      removed outlier: 4.507A  pdb=" N   ARG B 531 " --> pdb=" O   ILE B 173 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ILE B 539 " --> pdb=" O   ILE B 532 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TYR B 534 " --> pdb=" O   GLN B 537 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLU B 538 " --> pdb=" O   THR B 638 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   VAL B 640 " --> pdb=" O   GLU B 538 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL B 540 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   CYS B 642 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   PHE B 542 " --> pdb=" O   CYS B 642 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 181 through 184
      removed outlier: 4.063A  pdb=" N   SER B 182 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 282 through 287
    Processing sheet with id=AA4, first strand: chain 'B' and resid 296 through 300
      removed outlier: 4.302A  pdb=" N   TRP B 296 " --> pdb=" O   ILE B 307 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASP B 300 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLY B 303 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE B 339 " --> pdb=" O   GLU B 306 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 480 through 483
      removed outlier: 3.684A  pdb=" N   PHE B 399 " --> pdb=" O   TYR B 675 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TYR B 675 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 649 through 651
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1321 through 1327
      removed outlier: 6.879A  pdb=" N   PHE A1339 " --> pdb=" O   GLU A1323 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   LEU A1325 " --> pdb=" O   GLU A1337 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   GLU A1337 " --> pdb=" O   LEU A1325 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1501 through 1502
      removed outlier: 5.641A  pdb=" N   GLY A1485 " --> pdb=" O   LEU A1591 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2102 through 2106
      removed outlier: 7.028A  pdb=" N   ILE A2117 " --> pdb=" O   PRO A2104 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2162 through 2163

    268 hydrogen bonds defined for protein.
    771 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: 2.67

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2898
        1.34 -     1.47: 2185
        1.47 -     1.59: 4223
        1.59 -     1.72: 0
        1.72 -     1.84: 73
  Bond restraints: 9379
  Sorted by residual:
  bond pdb=" C   GLN A1628 "
       pdb=" N   PRO A1629 "
    ideal  model  delta    sigma   weight residual
    1.336  1.369 -0.033 9.80e-03 1.04e+04 1.15e+01
  bond pdb=" N   ILE A1712 "
       pdb=" CA  ILE A1712 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.99e+00
  bond pdb=" N   MET A1713 "
       pdb=" CA  MET A1713 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.28e-02 6.10e+03 8.53e+00
  bond pdb=" N   ASN A1714 "
       pdb=" CA  ASN A1714 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.29e-02 6.01e+03 8.31e+00
  bond pdb=" N   GLU A1717 "
       pdb=" CA  GLU A1717 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.25e-02 6.40e+03 6.62e+00
  ... (remaining 9374 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.35: 12103
        3.35 -     6.71: 512
        6.71 -    10.06: 75
       10.06 -    13.41: 23
       13.41 -    16.76: 5
  Bond angle restraints: 12718
  Sorted by residual:
  angle pdb=" N   PRO A2030 "
        pdb=" CA  PRO A2030 "
        pdb=" CB  PRO A2030 "
      ideal   model   delta    sigma   weight residual
     103.23  111.22   -7.99 1.07e+00 8.73e-01 5.58e+01
  angle pdb=" N   VAL A2047 "
        pdb=" CA  VAL A2047 "
        pdb=" C   VAL A2047 "
      ideal   model   delta    sigma   weight residual
     113.39  102.78   10.61 1.47e+00 4.63e-01 5.21e+01
  angle pdb=" C   TRP A1911 "
        pdb=" N   MET A1912 "
        pdb=" CA  MET A1912 "
      ideal   model   delta    sigma   weight residual
     122.08  134.52  -12.44 1.84e+00 2.95e-01 4.57e+01
  angle pdb=" N   ASN A1657 "
        pdb=" CA  ASN A1657 "
        pdb=" C   ASN A1657 "
      ideal   model   delta    sigma   weight residual
     110.80  125.14  -14.34 2.13e+00 2.20e-01 4.53e+01
  angle pdb=" C   SER A1896 "
        pdb=" N   TYR A1897 "
        pdb=" CA  TYR A1897 "
      ideal   model   delta    sigma   weight residual
     121.70  133.40  -11.70 1.80e+00 3.09e-01 4.23e+01
  ... (remaining 12713 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.77: 5116
       12.77 -    25.54: 436
       25.54 -    38.32: 100
       38.32 -    51.09: 22
       51.09 -    63.86: 2
  Dihedral angle restraints: 5676
    sinusoidal: 2194
      harmonic: 3482
  Sorted by residual:
  dihedral pdb=" C   ARG B 669 "
           pdb=" N   ARG B 669 "
           pdb=" CA  ARG B 669 "
           pdb=" CB  ARG B 669 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.36   14.76     0      2.50e+00 1.60e-01 3.48e+01
  dihedral pdb=" N   ARG B 669 "
           pdb=" C   ARG B 669 "
           pdb=" CA  ARG B 669 "
           pdb=" CB  ARG B 669 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.65  -13.85     0      2.50e+00 1.60e-01 3.07e+01
  dihedral pdb=" C   ASN A1714 "
           pdb=" N   ASN A1714 "
           pdb=" CA  ASN A1714 "
           pdb=" CB  ASN A1714 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.83   10.23     0      2.50e+00 1.60e-01 1.67e+01
  ... (remaining 5673 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1301
       0.111 -    0.222: 167
       0.222 -    0.332: 15
       0.332 -    0.443: 2
       0.443 -    0.554: 1
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" CA  ARG B 669 "
            pdb=" N   ARG B 669 "
            pdb=" C   ARG B 669 "
            pdb=" CB  ARG B 669 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.68e+00
  chirality pdb=" CB  ILE A1923 "
            pdb=" CA  ILE A1923 "
            pdb=" CG1 ILE A1923 "
            pdb=" CG2 ILE A1923 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CA  ASN A1657 "
            pdb=" N   ASN A1657 "
            pdb=" C   ASN A1657 "
            pdb=" CB  ASN A1657 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.89e+00
  ... (remaining 1483 not shown)

  Planarity restraints: 1606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 300 "    0.053 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO B 301 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO B 301 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 301 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1689 "   -0.018 2.00e-02 2.50e+03   1.91e-02 9.11e+00
        pdb=" CG  TRP A1689 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1689 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1689 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1689 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1689 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1689 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1689 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1689 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1689 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 458 "    0.019 2.00e-02 2.50e+03   2.09e-02 7.67e+00
        pdb=" CG  PHE B 458 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 458 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 458 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 458 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 458 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 458 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1603 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.16: 1
        2.16 -     2.84: 2978
        2.84 -     3.53: 12425
        3.53 -     4.21: 19684
        4.21 -     4.90: 31638
  Nonbonded interactions: 66726
  Sorted by model distance:
  nonbonded pdb=" N   CYS A2167 "
            pdb="ZN    ZN A2302 "
     model   vdw
     1.472 2.310
  nonbonded pdb=" O   VAL A1836 "
            pdb=" OG1 THR A1840 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OH  TYR A1317 "
            pdb=" O   SER A1320 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OE1 GLN A1435 "
            pdb=" OH  TYR A1670 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OH  TYR B 672 "
            pdb=" OE1 GLU B 685 "
     model   vdw
     2.277 3.040
  ... (remaining 66721 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
========== 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 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:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     24.470
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
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      :  0.009   0.106   9379  Z= 0.588
  Angle     :  1.616  16.763  12718  Z= 0.887
  Chirality :  0.077   0.554   1486
  Planarity :  0.008   0.080   1606
  Dihedral  : 10.198  63.859   3396
  Min Nonbonded Distance : 1.472

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 22.13 %
    Favored  : 77.26 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  5.63 %
    Favored  : 93.07 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    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: -4.84 (0.21), residues: 1148
  helix: -2.23 (0.23), residues: 321
  sheet: -3.81 (0.45), residues: 88
  loop : -3.85 (0.20), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.005   TRP A1689 
 HIS   0.017   0.004   HIS A2168 
 PHE   0.047   0.005   PHE B 458 
 TYR   0.040   0.004   TYR A1860 
 ARG   0.008   0.001   ARG B 543 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 329
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6293 (t0)
REVERT: B  183 TYR cc_start: 0.5785 (t80) cc_final: 0.5416 (t80)
REVERT: B  219 LEU cc_start: 0.9315 (mt) cc_final: 0.9089 (mt)
REVERT: B  352 ARG cc_start: 0.6809 (ttp-170) cc_final: 0.6098 (ttp-170)
REVERT: B  407 PHE cc_start: 0.8205 (m-80) cc_final: 0.7928 (m-80)
REVERT: B  419 LYS cc_start: 0.9053 (mttt) cc_final: 0.8710 (mmmm)
REVERT: B  455 SER cc_start: 0.9417 (p) cc_final: 0.8796 (t)
REVERT: B  510 SER cc_start: 0.8086 (p) cc_final: 0.7820 (t)
REVERT: B  627 ASP cc_start: 0.8587 (t0) cc_final: 0.8231 (t0)
REVERT: B  641 LEU cc_start: 0.8943 (mt) cc_final: 0.8119 (mt)
REVERT: A 1376 ILE cc_start: 0.8856 (mt) cc_final: 0.8415 (tp)
REVERT: A 1573 LEU cc_start: 0.9566 (tt) cc_final: 0.9112 (tp)
REVERT: A 1581 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8720 (tttt)
REVERT: A 1586 LEU cc_start: 0.8837 (mt) cc_final: 0.8498 (mm)
REVERT: A 1592 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8310 (tt)
REVERT: A 1800 ASP cc_start: 0.8799 (p0) cc_final: 0.8573 (p0)
REVERT: A 1906 TRP cc_start: 0.6221 (m100) cc_final: 0.5850 (m100)
REVERT: A 1929 GLU cc_start: 0.9337 (tt0) cc_final: 0.8850 (mp0)
REVERT: A 2162 LEU cc_start: 0.8384 (mt) cc_final: 0.7574 (mt)
REVERT: A 2196 GLN cc_start: 0.9118 (mt0) cc_final: 0.8903 (tt0)
REVERT: A 2197 LYS cc_start: 0.9068 (mttt) cc_final: 0.8647 (mmtt)
  outliers start: 13
  outliers final: 2
  residues processed: 336
  average time/residue: 0.2275
  time to fit residues: 104.0421
Evaluate side-chains
  227 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 223
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:   30.0000
   chunk 89 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 505 GLN
B 628 HIS
A1326 GLN
A1364 GLN
A1369 GLN
** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1413 ASN
A1435 GLN
A1575 GLN
A1609 GLN
** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1814 ASN
A1837 HIS
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2044 HIS
A2049 ASN
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.134060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.113013 restraints weight = 28593.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.115666 restraints weight = 19819.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.117543 restraints weight = 15068.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9379  Z= 0.250
  Angle     :  0.838   9.538  12718  Z= 0.430
  Chirality :  0.049   0.229   1486
  Planarity :  0.006   0.055   1606
  Dihedral  :  5.779  33.562   1240
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.33 %
    Favored  : 84.67 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.22 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -4.07 (0.22), residues: 1148
  helix: -1.10 (0.26), residues: 343
  sheet: -3.21 (0.48), residues: 103
  loop : -3.69 (0.21), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A1689 
 HIS   0.006   0.001   HIS A2168 
 PHE   0.024   0.002   PHE A1915 
 TYR   0.021   0.002   TYR A2207 
 ARG   0.004   0.001   ARG A2163 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 266
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 ARG cc_start: 0.6534 (tpp-160) cc_final: 0.6114 (tpp80)
REVERT: B  212 GLU cc_start: 0.9013 (pm20) cc_final: 0.8744 (pm20)
REVERT: B  214 LYS cc_start: 0.9316 (pttm) cc_final: 0.8940 (pttp)
REVERT: B  215 VAL cc_start: 0.9454 (m) cc_final: 0.8597 (m)
REVERT: B  219 LEU cc_start: 0.9294 (mt) cc_final: 0.9035 (mt)
REVERT: B  386 ARG cc_start: 0.9008 (mtm-85) cc_final: 0.8787 (mmm-85)
REVERT: B  398 LYS cc_start: 0.8153 (pttt) cc_final: 0.7898 (ttmt)
REVERT: B  407 PHE cc_start: 0.8324 (m-80) cc_final: 0.7782 (m-80)
REVERT: B  419 LYS cc_start: 0.9135 (mttt) cc_final: 0.8771 (mmmm)
REVERT: B  455 SER cc_start: 0.9377 (p) cc_final: 0.8852 (t)
REVERT: B  510 SER cc_start: 0.8151 (p) cc_final: 0.7917 (t)
REVERT: B  627 ASP cc_start: 0.8209 (t0) cc_final: 0.7974 (t0)
REVERT: B  639 MET cc_start: 0.7832 (ttp) cc_final: 0.7460 (ttt)
REVERT: B  641 LEU cc_start: 0.8909 (mt) cc_final: 0.8004 (mt)
REVERT: B  673 MET cc_start: 0.8019 (tpt) cc_final: 0.7660 (tpp)
REVERT: A 1679 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8417 (mmmt)
REVERT: A 1862 ASP cc_start: 0.8186 (t0) cc_final: 0.7857 (t0)
REVERT: A 1879 TYR cc_start: 0.8250 (t80) cc_final: 0.7897 (t80)
REVERT: A 1910 ILE cc_start: 0.7633 (mt) cc_final: 0.7432 (mt)
REVERT: A 1929 GLU cc_start: 0.8897 (tt0) cc_final: 0.8597 (mp0)
REVERT: A 2062 MET cc_start: 0.6595 (pmm) cc_final: 0.6163 (mpp)
REVERT: A 2173 ASP cc_start: 0.8415 (p0) cc_final: 0.8142 (p0)
REVERT: A 2197 LYS cc_start: 0.8850 (mttt) cc_final: 0.8623 (mmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 267
  average time/residue: 0.2445
  time to fit residues: 87.2708
Evaluate side-chains
  208 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 80 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 115 optimal weight:    0.5980
   chunk 57 optimal weight:   20.0000
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 GLN
B 474 ASN
B 505 GLN
B 609 GLN
A1364 GLN
** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1608 ASN
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2139 GLN
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.130517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.109865 restraints weight = 29313.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.112455 restraints weight = 20404.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.114330 restraints weight = 15480.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9379  Z= 0.271
  Angle     :  0.811   9.171  12718  Z= 0.416
  Chirality :  0.048   0.204   1486
  Planarity :  0.005   0.051   1606
  Dihedral  :  5.855  33.571   1240
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.81 %
    Favored  : 83.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    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: -3.63 (0.23), residues: 1148
  helix: -0.37 (0.28), residues: 338
  sheet: -2.72 (0.48), residues: 102
  loop : -3.66 (0.21), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A1689 
 HIS   0.008   0.002   HIS A2168 
 PHE   0.022   0.002   PHE B 192 
 TYR   0.018   0.002   TYR A2207 
 ARG   0.007   0.001   ARG A1890 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  214 LYS cc_start: 0.9258 (pttp) cc_final: 0.8986 (pttp)
REVERT: B  219 LEU cc_start: 0.9332 (mt) cc_final: 0.9027 (mt)
REVERT: B  407 PHE cc_start: 0.8324 (m-80) cc_final: 0.7905 (m-80)
REVERT: B  419 LYS cc_start: 0.9113 (mttt) cc_final: 0.8761 (mmmm)
REVERT: B  455 SER cc_start: 0.9457 (p) cc_final: 0.8976 (t)
REVERT: B  641 LEU cc_start: 0.8902 (mt) cc_final: 0.8675 (mt)
REVERT: A 1484 ILE cc_start: 0.7585 (tp) cc_final: 0.7253 (tp)
REVERT: A 1487 LEU cc_start: 0.9239 (tt) cc_final: 0.9031 (tt)
REVERT: A 1573 LEU cc_start: 0.9622 (tp) cc_final: 0.9375 (tp)
REVERT: A 1578 THR cc_start: 0.9029 (p) cc_final: 0.8272 (p)
REVERT: A 1679 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8436 (mmmt)
REVERT: A 1865 GLN cc_start: 0.8281 (mp-120) cc_final: 0.7993 (mp-120)
REVERT: A 1879 TYR cc_start: 0.8478 (t80) cc_final: 0.8183 (t80)
REVERT: A 1929 GLU cc_start: 0.9127 (tt0) cc_final: 0.8748 (mp0)
REVERT: A 2173 ASP cc_start: 0.8424 (p0) cc_final: 0.8223 (p0)
REVERT: A 2197 LYS cc_start: 0.8981 (mttt) cc_final: 0.8693 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2307
  time to fit residues: 77.9974
Evaluate side-chains
  205 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 91 optimal weight:    0.4980
   chunk 18 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 ASN
B 505 GLN
B 611 HIS
A1373 ASN
A1435 GLN
A1575 GLN
A1609 GLN
A1662 ASN
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.133482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.112444 restraints weight = 28577.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.115101 restraints weight = 19809.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.117050 restraints weight = 15017.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9379  Z= 0.202
  Angle     :  0.758  11.127  12718  Z= 0.383
  Chirality :  0.047   0.219   1486
  Planarity :  0.005   0.050   1606
  Dihedral  :  5.785  34.138   1240
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.46 %
    Favored  : 85.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    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: -3.33 (0.24), residues: 1148
  helix:  0.05 (0.29), residues: 340
  sheet: -2.51 (0.50), residues: 111
  loop : -3.59 (0.22), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A1689 
 HIS   0.004   0.001   HIS A2168 
 PHE   0.024   0.002   PHE B 282 
 TYR   0.015   0.002   TYR A1486 
 ARG   0.005   0.001   ARG A1664 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  170 PHE cc_start: 0.8185 (t80) cc_final: 0.7792 (p90)
REVERT: B  212 GLU cc_start: 0.9024 (pm20) cc_final: 0.8820 (pm20)
REVERT: B  214 LYS cc_start: 0.9200 (pttp) cc_final: 0.8941 (pttp)
REVERT: B  219 LEU cc_start: 0.9275 (mt) cc_final: 0.9004 (mt)
REVERT: B  289 ASN cc_start: 0.9029 (m110) cc_final: 0.7583 (t0)
REVERT: B  398 LYS cc_start: 0.8148 (pttt) cc_final: 0.7941 (ttmt)
REVERT: B  419 LYS cc_start: 0.9064 (mttt) cc_final: 0.8755 (mmmm)
REVERT: B  455 SER cc_start: 0.9445 (p) cc_final: 0.8969 (t)
REVERT: B  482 ILE cc_start: 0.8456 (mt) cc_final: 0.8220 (mt)
REVERT: B  639 MET cc_start: 0.7753 (ttp) cc_final: 0.7545 (ttt)
REVERT: B  641 LEU cc_start: 0.8877 (mt) cc_final: 0.8068 (mt)
REVERT: B  673 MET cc_start: 0.7890 (tpp) cc_final: 0.7645 (tpp)
REVERT: A 1487 LEU cc_start: 0.9228 (tt) cc_final: 0.9017 (tt)
REVERT: A 1578 THR cc_start: 0.8688 (p) cc_final: 0.8395 (p)
REVERT: A 1679 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8432 (mmmt)
REVERT: A 1865 GLN cc_start: 0.8262 (mp-120) cc_final: 0.7956 (mp10)
REVERT: A 1876 GLU cc_start: 0.9018 (tt0) cc_final: 0.8722 (tt0)
REVERT: A 1910 ILE cc_start: 0.7769 (mt) cc_final: 0.7514 (mt)
REVERT: A 1912 MET cc_start: 0.5984 (ttm) cc_final: 0.5663 (ttm)
REVERT: A 1929 GLU cc_start: 0.8947 (tt0) cc_final: 0.8649 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2386
  time to fit residues: 79.2017
Evaluate side-chains
  206 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 68 optimal weight:    0.0010
   chunk 24 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 108 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 69 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.2190

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

Flipped N/Q/H residues before XYZ refinement:
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1326 GLN
A1373 ASN
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2143 GLN ** 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 = 0.3995 r_free = 0.3995 target = 0.134494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.113653 restraints weight = 28894.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.116269 restraints weight = 20239.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.118219 restraints weight = 15455.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9379  Z= 0.187
  Angle     :  0.748   9.695  12718  Z= 0.371
  Chirality :  0.047   0.205   1486
  Planarity :  0.004   0.051   1606
  Dihedral  :  5.657  34.213   1240
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.94 %
    Favored  : 86.06 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.01 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.12 (0.24), residues: 1148
  helix:  0.33 (0.29), residues: 340
  sheet: -2.23 (0.60), residues: 83
  loop : -3.52 (0.21), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP A1689 
 HIS   0.004   0.001   HIS A1352 
 PHE   0.014   0.001   PHE B 458 
 TYR   0.015   0.002   TYR A1486 
 ARG   0.007   0.001   ARG A1664 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 247
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  183 TYR cc_start: 0.6430 (t80) cc_final: 0.5960 (t80)
REVERT: B  212 GLU cc_start: 0.9005 (pm20) cc_final: 0.8787 (pm20)
REVERT: B  219 LEU cc_start: 0.9245 (mt) cc_final: 0.8980 (mt)
REVERT: B  289 ASN cc_start: 0.8996 (m110) cc_final: 0.7566 (t0)
REVERT: B  419 LYS cc_start: 0.8960 (mttt) cc_final: 0.8664 (mmmm)
REVERT: B  420 ILE cc_start: 0.9587 (mt) cc_final: 0.9380 (tt)
REVERT: B  455 SER cc_start: 0.9394 (p) cc_final: 0.8908 (t)
REVERT: B  482 ILE cc_start: 0.8461 (mt) cc_final: 0.8243 (mt)
REVERT: B  635 ILE cc_start: 0.8691 (mm) cc_final: 0.8306 (mm)
REVERT: B  673 MET cc_start: 0.7864 (tpp) cc_final: 0.7614 (tpp)
REVERT: A 1353 ILE cc_start: 0.8040 (mm) cc_final: 0.7671 (tp)
REVERT: A 1439 MET cc_start: 0.8366 (pmm) cc_final: 0.7421 (pmm)
REVERT: A 1487 LEU cc_start: 0.9165 (tt) cc_final: 0.8955 (tt)
REVERT: A 1573 LEU cc_start: 0.9598 (tp) cc_final: 0.9297 (tp)
REVERT: A 1578 THR cc_start: 0.8665 (p) cc_final: 0.8191 (p)
REVERT: A 1679 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8398 (mmmt)
REVERT: A 1865 GLN cc_start: 0.8121 (mp-120) cc_final: 0.7825 (mp-120)
REVERT: A 1876 GLU cc_start: 0.8940 (tt0) cc_final: 0.8411 (tt0)
REVERT: A 1910 ILE cc_start: 0.7414 (mt) cc_final: 0.7194 (mt)
REVERT: A 1912 MET cc_start: 0.5866 (ttm) cc_final: 0.5597 (ttm)
REVERT: A 1915 PHE cc_start: 0.6333 (p90) cc_final: 0.5950 (p90)
REVERT: A 1920 LEU cc_start: 0.7738 (pp) cc_final: 0.7232 (pp)
REVERT: A 1929 GLU cc_start: 0.8817 (tt0) cc_final: 0.8552 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2356
  time to fit residues: 78.5684
Evaluate side-chains
  205 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN
B 340 HIS
B 474 ASN
A1575 GLN
A1662 ASN
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2145 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.130472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.109903 restraints weight = 29763.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.112452 restraints weight = 20688.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.114211 restraints weight = 15770.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9379  Z= 0.281
  Angle     :  0.799   9.537  12718  Z= 0.406
  Chirality :  0.048   0.182   1486
  Planarity :  0.005   0.055   1606
  Dihedral  :  6.010  36.201   1240
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.55 %
    Favored  : 83.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    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: -3.21 (0.24), residues: 1148
  helix:  0.24 (0.28), residues: 354
  sheet: -2.56 (0.56), residues: 92
  loop : -3.61 (0.21), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP A1689 
 HIS   0.009   0.002   HIS A2168 
 PHE   0.022   0.002   PHE B 192 
 TYR   0.017   0.002   TYR A1879 
 ARG   0.010   0.001   ARG B 352 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 GLN cc_start: 0.5766 (tt0) cc_final: 0.5341 (tt0)
REVERT: B  183 TYR cc_start: 0.6221 (t80) cc_final: 0.5698 (t80)
REVERT: B  215 VAL cc_start: 0.9405 (m) cc_final: 0.8666 (m)
REVERT: B  219 LEU cc_start: 0.9287 (mt) cc_final: 0.8993 (mt)
REVERT: B  407 PHE cc_start: 0.8393 (m-80) cc_final: 0.8029 (m-80)
REVERT: B  410 ASP cc_start: 0.7304 (t0) cc_final: 0.7036 (t0)
REVERT: B  419 LYS cc_start: 0.9016 (mttt) cc_final: 0.8723 (mmmm)
REVERT: B  455 SER cc_start: 0.9455 (p) cc_final: 0.8987 (t)
REVERT: B  482 ILE cc_start: 0.8511 (mt) cc_final: 0.8257 (mt)
REVERT: A 1353 ILE cc_start: 0.7946 (mm) cc_final: 0.7636 (tp)
REVERT: A 1439 MET cc_start: 0.8514 (pmm) cc_final: 0.7968 (pmm)
REVERT: A 1487 LEU cc_start: 0.9116 (tt) cc_final: 0.8890 (tt)
REVERT: A 1570 TYR cc_start: 0.7971 (t80) cc_final: 0.7771 (t80)
REVERT: A 1573 LEU cc_start: 0.9612 (tp) cc_final: 0.9324 (tp)
REVERT: A 1614 LYS cc_start: 0.4352 (tmtt) cc_final: 0.3369 (tttt)
REVERT: A 1679 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8515 (mmmt)
REVERT: A 1876 GLU cc_start: 0.8969 (tt0) cc_final: 0.8554 (tt0)
REVERT: A 1906 TRP cc_start: 0.6269 (m100) cc_final: 0.5663 (m100)
REVERT: A 1910 ILE cc_start: 0.7709 (mt) cc_final: 0.7478 (mt)
REVERT: A 1929 GLU cc_start: 0.8893 (tt0) cc_final: 0.8620 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2189
  time to fit residues: 73.1025
Evaluate side-chains
  199 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 109 optimal weight:    0.0000
   chunk 93 optimal weight:    0.4980
   chunk 45 optimal weight:   10.0000
   chunk 111 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0040
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
B 474 ASN
B 611 HIS
A1326 GLN
A1575 GLN
** A1703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2145 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.136132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.115607 restraints weight = 28894.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.118199 restraints weight = 20122.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.120080 restraints weight = 15295.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.4985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9379  Z= 0.174
  Angle     :  0.746   9.597  12718  Z= 0.370
  Chirality :  0.046   0.213   1486
  Planarity :  0.004   0.046   1606
  Dihedral  :  5.652  34.909   1240
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.63 %
    Favored  : 87.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.25), residues: 1148
  helix:  0.60 (0.29), residues: 343
  sheet: -2.36 (0.55), residues: 99
  loop : -3.42 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1689 
 HIS   0.009   0.001   HIS A2145 
 PHE   0.019   0.002   PHE A1718 
 TYR   0.014   0.001   TYR A1486 
 ARG   0.005   0.001   ARG B 180 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 ARG cc_start: 0.6490 (tpp-160) cc_final: 0.6004 (tpp80)
REVERT: B  183 TYR cc_start: 0.6504 (t80) cc_final: 0.6044 (t80)
REVERT: B  188 MET cc_start: 0.6717 (mtt) cc_final: 0.6196 (mtt)
REVERT: B  212 GLU cc_start: 0.9075 (pm20) cc_final: 0.8802 (pm20)
REVERT: B  215 VAL cc_start: 0.9100 (m) cc_final: 0.8727 (m)
REVERT: B  219 LEU cc_start: 0.9111 (mt) cc_final: 0.8807 (mt)
REVERT: B  226 ASN cc_start: 0.9080 (t0) cc_final: 0.8871 (t0)
REVERT: B  230 MET cc_start: 0.8983 (mmp) cc_final: 0.8696 (mmm)
REVERT: B  289 ASN cc_start: 0.8902 (m110) cc_final: 0.7528 (t0)
REVERT: B  402 LEU cc_start: 0.9144 (mm) cc_final: 0.8942 (mm)
REVERT: B  410 ASP cc_start: 0.7341 (t0) cc_final: 0.7095 (t70)
REVERT: B  419 LYS cc_start: 0.8892 (mttt) cc_final: 0.8623 (mmmm)
REVERT: B  641 LEU cc_start: 0.8874 (mt) cc_final: 0.7870 (mt)
REVERT: A 1353 ILE cc_start: 0.7847 (mm) cc_final: 0.7444 (tp)
REVERT: A 1439 MET cc_start: 0.8405 (pmm) cc_final: 0.7478 (pmm)
REVERT: A 1573 LEU cc_start: 0.9586 (tp) cc_final: 0.9172 (tp)
REVERT: A 1578 THR cc_start: 0.8865 (t) cc_final: 0.8631 (t)
REVERT: A 1614 LYS cc_start: 0.4230 (tmtt) cc_final: 0.3334 (tttt)
REVERT: A 1876 GLU cc_start: 0.8795 (tt0) cc_final: 0.8425 (tt0)
REVERT: A 1910 ILE cc_start: 0.7288 (mt) cc_final: 0.7044 (mt)
REVERT: A 1929 GLU cc_start: 0.8734 (tt0) cc_final: 0.8520 (mp0)
REVERT: A 2062 MET cc_start: 0.6967 (pmm) cc_final: 0.6505 (mpp)
REVERT: A 2152 SER cc_start: 0.9135 (t) cc_final: 0.8655 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2263
  time to fit residues: 74.6628
Evaluate side-chains
  193 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0570
   chunk 113 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 106 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    2.3904

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

Flipped N/Q/H residues before XYZ refinement:
B 474 ASN
A1326 GLN
A1575 GLN
A1865 GLN
** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.132392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.111968 restraints weight = 29706.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.114602 restraints weight = 20665.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.116505 restraints weight = 15730.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.5137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9379  Z= 0.231
  Angle     :  0.770   9.370  12718  Z= 0.390
  Chirality :  0.048   0.248   1486
  Planarity :  0.005   0.053   1606
  Dihedral  :  5.812  37.177   1240
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.37 %
    Favored  : 85.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.25), residues: 1148
  helix:  0.63 (0.29), residues: 344
  sheet: -2.41 (0.54), residues: 99
  loop : -3.47 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1689 
 HIS   0.006   0.001   HIS A2168 
 PHE   0.017   0.002   PHE B 170 
 TYR   0.018   0.002   TYR A1879 
 ARG   0.004   0.001   ARG A2166 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 ARG cc_start: 0.6757 (tpp-160) cc_final: 0.6094 (tpp80)
REVERT: B  183 TYR cc_start: 0.6415 (t80) cc_final: 0.5852 (t80)
REVERT: B  188 MET cc_start: 0.6521 (mtt) cc_final: 0.5984 (mtt)
REVERT: B  226 ASN cc_start: 0.9181 (t0) cc_final: 0.8917 (t0)
REVERT: B  230 MET cc_start: 0.9098 (mmp) cc_final: 0.8762 (mmm)
REVERT: B  289 ASN cc_start: 0.8989 (m110) cc_final: 0.7559 (t0)
REVERT: B  407 PHE cc_start: 0.8484 (m-80) cc_final: 0.8090 (m-80)
REVERT: B  410 ASP cc_start: 0.7543 (t0) cc_final: 0.7329 (t0)
REVERT: B  414 MET cc_start: 0.8860 (mpp) cc_final: 0.8477 (mpp)
REVERT: B  422 GLN cc_start: 0.9101 (tt0) cc_final: 0.8440 (mm-40)
REVERT: B  510 SER cc_start: 0.8281 (t) cc_final: 0.8063 (t)
REVERT: B  628 HIS cc_start: 0.8623 (t70) cc_final: 0.8331 (t70)
REVERT: B  673 MET cc_start: 0.7914 (tpp) cc_final: 0.7709 (tpp)
REVERT: A 1353 ILE cc_start: 0.7774 (mm) cc_final: 0.7448 (tp)
REVERT: A 1364 GLN cc_start: 0.8343 (tp40) cc_final: 0.8135 (tp40)
REVERT: A 1439 MET cc_start: 0.8482 (pmm) cc_final: 0.7625 (pmm)
REVERT: A 1570 TYR cc_start: 0.8103 (t80) cc_final: 0.7742 (t80)
REVERT: A 1578 THR cc_start: 0.8876 (t) cc_final: 0.8419 (t)
REVERT: A 1614 LYS cc_start: 0.4278 (tmtt) cc_final: 0.3313 (tttt)
REVERT: A 1876 GLU cc_start: 0.8924 (tt0) cc_final: 0.8589 (tt0)
REVERT: A 1899 ASP cc_start: 0.7084 (t70) cc_final: 0.6812 (t0)
REVERT: A 1910 ILE cc_start: 0.7409 (mt) cc_final: 0.7185 (mt)
REVERT: A 1912 MET cc_start: 0.7101 (ttt) cc_final: 0.6860 (ttm)
REVERT: A 1920 LEU cc_start: 0.7951 (pp) cc_final: 0.7531 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2098
  time to fit residues: 66.9508
Evaluate side-chains
  188 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 88 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 93 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A1865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2060 HIS
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2145 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.130789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.110297 restraints weight = 29558.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.112716 restraints weight = 20956.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.114465 restraints weight = 16161.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.5223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9379  Z= 0.283
  Angle     :  0.826   9.825  12718  Z= 0.420
  Chirality :  0.050   0.255   1486
  Planarity :  0.005   0.070   1606
  Dihedral  :  6.169  39.089   1240
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.42 %
    Favored  : 84.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    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: -3.08 (0.24), residues: 1148
  helix:  0.38 (0.28), residues: 356
  sheet: -2.42 (0.56), residues: 92
  loop : -3.57 (0.21), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP A1906 
 HIS   0.009   0.002   HIS A2168 
 PHE   0.021   0.002   PHE B 192 
 TYR   0.016   0.002   TYR B 534 
 ARG   0.006   0.001   ARG B 352 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  183 TYR cc_start: 0.6300 (t80) cc_final: 0.5735 (t80)
REVERT: B  188 MET cc_start: 0.6449 (mtt) cc_final: 0.5829 (mtt)
REVERT: B  212 GLU cc_start: 0.8985 (pm20) cc_final: 0.8573 (pm20)
REVERT: B  219 LEU cc_start: 0.9110 (mt) cc_final: 0.8882 (mt)
REVERT: B  226 ASN cc_start: 0.9200 (t0) cc_final: 0.8916 (t0)
REVERT: B  230 MET cc_start: 0.9176 (mmp) cc_final: 0.8803 (mmm)
REVERT: B  289 ASN cc_start: 0.9109 (m110) cc_final: 0.7703 (t0)
REVERT: B  407 PHE cc_start: 0.8433 (m-80) cc_final: 0.8011 (m-80)
REVERT: B  410 ASP cc_start: 0.7521 (t0) cc_final: 0.7250 (t0)
REVERT: B  414 MET cc_start: 0.8842 (mpp) cc_final: 0.8624 (mpp)
REVERT: B  419 LYS cc_start: 0.9033 (mttt) cc_final: 0.8727 (mmmm)
REVERT: B  422 GLN cc_start: 0.9103 (tt0) cc_final: 0.8435 (mm-40)
REVERT: B  628 HIS cc_start: 0.8650 (t70) cc_final: 0.8430 (t70)
REVERT: B  673 MET cc_start: 0.7889 (tpp) cc_final: 0.7681 (tpp)
REVERT: A 1353 ILE cc_start: 0.7791 (mm) cc_final: 0.7571 (tp)
REVERT: A 1439 MET cc_start: 0.8559 (pmm) cc_final: 0.8003 (pmm)
REVERT: A 1487 LEU cc_start: 0.9128 (tt) cc_final: 0.8920 (tt)
REVERT: A 1570 TYR cc_start: 0.8159 (t80) cc_final: 0.7904 (t80)
REVERT: A 1578 THR cc_start: 0.8819 (t) cc_final: 0.8348 (t)
REVERT: A 1614 LYS cc_start: 0.4791 (tmtt) cc_final: 0.3777 (tttt)
REVERT: A 1876 GLU cc_start: 0.8977 (tt0) cc_final: 0.8774 (tt0)
REVERT: A 1899 ASP cc_start: 0.7292 (t70) cc_final: 0.7068 (t0)
REVERT: A 2144 GLU cc_start: 0.7288 (tm-30) cc_final: 0.7021 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2095
  time to fit residues: 67.7673
Evaluate side-chains
  195 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   chunk 95 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 106 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
B 474 ASN
** A1806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.132342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.111874 restraints weight = 29434.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.114217 restraints weight = 21047.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.115942 restraints weight = 16360.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.5412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9379  Z= 0.217
  Angle     :  0.809  10.733  12718  Z= 0.406
  Chirality :  0.050   0.255   1486
  Planarity :  0.004   0.046   1606
  Dihedral  :  6.033  37.926   1240
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.68 %
    Favored  : 86.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    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: -3.01 (0.24), residues: 1148
  helix:  0.31 (0.28), residues: 363
  sheet: -2.05 (0.59), residues: 89
  loop : -3.53 (0.21), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1689 
 HIS   0.007   0.001   HIS A2145 
 PHE   0.020   0.002   PHE B 218 
 TYR   0.022   0.002   TYR A1879 
 ARG   0.007   0.001   ARG A2166 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  183 TYR cc_start: 0.6472 (t80) cc_final: 0.6007 (t80)
REVERT: B  188 MET cc_start: 0.6452 (mtt) cc_final: 0.5837 (mtt)
REVERT: B  212 GLU cc_start: 0.8929 (pm20) cc_final: 0.8517 (pm20)
REVERT: B  219 LEU cc_start: 0.9203 (mt) cc_final: 0.8898 (mt)
REVERT: B  223 TYR cc_start: 0.8529 (m-10) cc_final: 0.7948 (m-10)
REVERT: B  226 ASN cc_start: 0.9079 (t0) cc_final: 0.8844 (t0)
REVERT: B  230 MET cc_start: 0.9062 (mmp) cc_final: 0.8746 (mmm)
REVERT: B  289 ASN cc_start: 0.8986 (m110) cc_final: 0.7602 (t0)
REVERT: B  407 PHE cc_start: 0.8488 (m-80) cc_final: 0.8083 (m-80)
REVERT: B  410 ASP cc_start: 0.7557 (t0) cc_final: 0.7258 (t70)
REVERT: B  419 LYS cc_start: 0.8983 (mttt) cc_final: 0.8758 (mmmm)
REVERT: B  422 GLN cc_start: 0.9118 (tt0) cc_final: 0.8141 (mm-40)
REVERT: B  673 MET cc_start: 0.7854 (tpp) cc_final: 0.7629 (tpp)
REVERT: A 1332 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8012 (mm-30)
REVERT: A 1439 MET cc_start: 0.8534 (pmm) cc_final: 0.7959 (pmm)
REVERT: A 1470 MET cc_start: 0.7214 (mtt) cc_final: 0.6951 (mmt)
REVERT: A 1570 TYR cc_start: 0.8272 (t80) cc_final: 0.7968 (t80)
REVERT: A 1614 LYS cc_start: 0.4557 (tmtt) cc_final: 0.3557 (tttt)
REVERT: A 1899 ASP cc_start: 0.7186 (t70) cc_final: 0.6834 (t0)
REVERT: A 1910 ILE cc_start: 0.7335 (mt) cc_final: 0.7113 (mt)
REVERT: A 2144 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6865 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.2046
  time to fit residues: 66.5663
Evaluate side-chains
  194 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 73 optimal weight:    0.7980
   chunk 103 optimal weight:   10.0000
   chunk 100 optimal weight:    0.0570
   overall best weight:    1.9704

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

Flipped N/Q/H residues before XYZ refinement:
B 474 ASN
** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.132081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.111478 restraints weight = 29318.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.113858 restraints weight = 20795.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.115579 restraints weight = 16072.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.5518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9379  Z= 0.213
  Angle     :  0.789  10.629  12718  Z= 0.395
  Chirality :  0.049   0.250   1486
  Planarity :  0.004   0.048   1606
  Dihedral  :  5.946  37.918   1240
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.85 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.25), residues: 1148
  helix:  0.43 (0.29), residues: 357
  sheet: -1.99 (0.59), residues: 89
  loop : -3.49 (0.21), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A1906 
 HIS   0.007   0.001   HIS A2145 
 PHE   0.018   0.002   PHE B 550 
 TYR   0.015   0.002   TYR A1486 
 ARG   0.007   0.001   ARG A2166 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2828.30 seconds
wall clock time: 51 minutes 39.67 seconds (3099.67 seconds total)