Starting phenix.real_space_refine
on Wed Sep 17 14:54:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hv8_0287/09_2025/6hv8_0287.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hv8_0287/09_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_0287/09_2025/6hv8_0287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hv8_0287/09_2025/6hv8_0287.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hv8_0287/09_2025/6hv8_0287.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hv8_0287/09_2025/6hv8_0287.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'HIS:plan': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 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, 'TYR:plan': 5, 'GLU:plan': 11, 'PHE:plan': 8, 'ARG:plan': 4, 'ASP:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1}
          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: 2.41, per 1000 atoms: 0.26
  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: 0.89
  Conformation dependent library (CDL) restraints added in 395.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 0.37
  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: 1.50

  Time building geometry restraints manager: 1.19 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:             0.530
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.620
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.800
-------------------------------------------------------------------------------
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      :  0.011   0.409   9387  Z= 0.471
  Angle     :  1.952  72.608  12730  Z= 0.909
  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 : 8.91
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG B 543 
 TYR   0.040   0.004   TYR A1860 
 PHE   0.047   0.005   PHE B 458 
 TRP   0.052   0.005   TRP A1689 
 HIS   0.017   0.004   HIS A2168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00897 ( 9379)
  covalent geometry    : angle       1.61647 (12718)
  hydrogen bonds       : bond        0.16721 (  268)
  hydrogen bonds       : angle       7.78765 (  771)
  metal coordination   : bond        0.19418 (    8)
  metal coordination   : angle      35.69237 (   12)

*********************** 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  : 0.314 
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: 0.1012
  time to fit residues: 46.5915
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  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B 505 GLN
B 609 GLN
B 628 HIS
A1326 GLN
A1364 GLN
A1369 GLN
** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1413 ASN
A1575 GLN
A1609 GLN
A1742 ASN
A1814 ASN
A1837 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 = 0.4016 r_free = 0.4016 target = 0.136300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.115001 restraints weight = 28296.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.117740 restraints weight = 19599.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.119692 restraints weight = 14840.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.121146 restraints weight = 11992.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.122051 restraints weight = 10162.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9387  Z= 0.154
  Angle     :  0.970  40.522  12730  Z= 0.429
  Chirality :  0.048   0.233   1486
  Planarity :  0.006   0.055   1606
  Dihedral  :  5.666  35.010   1240
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 14.55 %
    Favored  : 85.37 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.32 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.04 (0.22), residues: 1148
  helix: -1.12 (0.25), residues: 343
  sheet: -3.03 (0.49), residues: 100
  loop : -3.67 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1664 
 TYR   0.019   0.002   TYR A2207 
 PHE   0.023   0.002   PHE A1915 
 TRP   0.039   0.002   TRP A1689 
 HIS   0.005   0.001   HIS A2168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9379)
  covalent geometry    : angle       0.81826 (12718)
  hydrogen bonds       : bond        0.04952 (  268)
  hydrogen bonds       : angle       5.95392 (  771)
  metal coordination   : bond        0.01993 (    8)
  metal coordination   : angle      16.96825 (   12)

*********************** 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
  269 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 268
  time to evaluate  : 0.370 
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  180 ARG cc_start: 0.6480 (tpp-160) cc_final: 0.6119 (tpp80)
REVERT: B  212 GLU cc_start: 0.8933 (pm20) cc_final: 0.8685 (pm20)
REVERT: B  214 LYS cc_start: 0.9256 (pttm) cc_final: 0.8895 (pttp)
REVERT: B  215 VAL cc_start: 0.9445 (m) cc_final: 0.8571 (m)
REVERT: B  219 LEU cc_start: 0.9290 (mt) cc_final: 0.9032 (mt)
REVERT: B  386 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8665 (mmm-85)
REVERT: B  398 LYS cc_start: 0.8105 (pttt) cc_final: 0.7881 (ttmt)
REVERT: B  407 PHE cc_start: 0.8302 (m-80) cc_final: 0.7787 (m-80)
REVERT: B  419 LYS cc_start: 0.9089 (mttt) cc_final: 0.8766 (mmmm)
REVERT: B  510 SER cc_start: 0.8052 (p) cc_final: 0.7851 (t)
REVERT: B  608 ASP cc_start: 0.7721 (m-30) cc_final: 0.7506 (m-30)
REVERT: B  627 ASP cc_start: 0.8092 (t0) cc_final: 0.7809 (t0)
REVERT: B  673 MET cc_start: 0.7950 (tpt) cc_final: 0.7687 (tpp)
REVERT: A 1579 LYS cc_start: 0.9331 (ttpt) cc_final: 0.9122 (tptp)
REVERT: A 1679 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8481 (mmmt)
REVERT: A 1860 TYR cc_start: 0.7421 (t80) cc_final: 0.7161 (t80)
REVERT: A 1865 GLN cc_start: 0.8187 (mp-120) cc_final: 0.7966 (mp-120)
REVERT: A 1879 TYR cc_start: 0.8109 (t80) cc_final: 0.7681 (t80)
REVERT: A 1910 ILE cc_start: 0.7563 (mt) cc_final: 0.7338 (mt)
REVERT: A 1929 GLU cc_start: 0.8704 (tt0) cc_final: 0.8492 (mp0)
REVERT: A 2062 MET cc_start: 0.6849 (pmm) cc_final: 0.6247 (mpp)
REVERT: A 2117 ILE cc_start: 0.9138 (mm) cc_final: 0.8931 (tp)
REVERT: A 2173 ASP cc_start: 0.8386 (p0) cc_final: 0.8149 (p0)
REVERT: A 2197 LYS cc_start: 0.8821 (mttt) cc_final: 0.8563 (mmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 268
  average time/residue: 0.1119
  time to fit residues: 40.3510
Evaluate side-chains
  214 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 108 optimal weight:    6.9990
   chunk 115 optimal weight:    6.9990
   chunk 87 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 105 optimal weight:    0.3980
   chunk 106 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 40 optimal weight:    7.9990
   overall best weight:    3.3986

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

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN
B 474 ASN
A1364 GLN
** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1575 GLN
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.130188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.109496 restraints weight = 29620.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.112098 restraints weight = 20773.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.113968 restraints weight = 15817.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.115309 restraints weight = 12810.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.116344 restraints weight = 10893.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9387  Z= 0.207
  Angle     :  0.947  32.348  12730  Z= 0.435
  Chirality :  0.049   0.198   1486
  Planarity :  0.005   0.051   1606
  Dihedral  :  5.842  33.146   1240
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.16 %
    Favored  : 82.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.67 (0.23), residues: 1148
  helix: -0.43 (0.27), residues: 342
  sheet: -2.73 (0.47), residues: 101
  loop : -3.69 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1664 
 TYR   0.019   0.002   TYR A1881 
 PHE   0.025   0.002   PHE A1339 
 TRP   0.029   0.002   TRP A1689 
 HIS   0.008   0.002   HIS A2168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 9379)
  covalent geometry    : angle       0.83111 (12718)
  hydrogen bonds       : bond        0.04713 (  268)
  hydrogen bonds       : angle       5.67905 (  771)
  metal coordination   : bond        0.01441 (    8)
  metal coordination   : angle      14.83423 (   12)

*********************** 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
  244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.380 
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  214 LYS cc_start: 0.9418 (pttp) cc_final: 0.9135 (pttp)
REVERT: B  219 LEU cc_start: 0.9267 (mt) cc_final: 0.8988 (mt)
REVERT: B  398 LYS cc_start: 0.8254 (pttt) cc_final: 0.7988 (ttmt)
REVERT: B  407 PHE cc_start: 0.8319 (m-80) cc_final: 0.7879 (m-80)
REVERT: B  419 LYS cc_start: 0.9086 (mttt) cc_final: 0.8774 (mmmm)
REVERT: B  429 PRO cc_start: 0.8730 (Cg_endo) cc_final: 0.8387 (Cg_exo)
REVERT: B  455 SER cc_start: 0.9423 (p) cc_final: 0.8900 (t)
REVERT: A 1323 GLU cc_start: 0.8002 (pm20) cc_final: 0.7727 (pm20)
REVERT: A 1470 MET cc_start: 0.7360 (mtt) cc_final: 0.7109 (mtt)
REVERT: A 1484 ILE cc_start: 0.7423 (tp) cc_final: 0.7144 (tp)
REVERT: A 1487 LEU cc_start: 0.9224 (tt) cc_final: 0.9015 (tt)
REVERT: A 1573 LEU cc_start: 0.9615 (tp) cc_final: 0.9337 (tp)
REVERT: A 1578 THR cc_start: 0.8988 (p) cc_final: 0.8198 (p)
REVERT: A 1679 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8478 (mmmt)
REVERT: A 1827 LEU cc_start: 0.7563 (tt) cc_final: 0.7311 (mm)
REVERT: A 1860 TYR cc_start: 0.7766 (t80) cc_final: 0.7429 (t80)
REVERT: A 1879 TYR cc_start: 0.8392 (t80) cc_final: 0.8140 (t80)
REVERT: A 1929 GLU cc_start: 0.9104 (tt0) cc_final: 0.8643 (mp0)
REVERT: A 2173 ASP cc_start: 0.8358 (p0) cc_final: 0.8148 (p0)
REVERT: A 2197 LYS cc_start: 0.8952 (mttt) cc_final: 0.8636 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1065
  time to fit residues: 35.5319
Evaluate side-chains
  196 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 32 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0040
   chunk 74 optimal weight:    0.0970
   chunk 17 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.6196

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

Flipped N/Q/H residues before XYZ refinement:
B 474 ASN
** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1575 GLN
A1662 ASN
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2044 HIS
** 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 = 0.3986 r_free = 0.3986 target = 0.134298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.112930 restraints weight = 29143.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.115660 restraints weight = 20330.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.117615 restraints weight = 15429.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.119058 restraints weight = 12478.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.120087 restraints weight = 10577.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9387  Z= 0.138
  Angle     :  0.852  28.649  12730  Z= 0.388
  Chirality :  0.047   0.210   1486
  Planarity :  0.004   0.049   1606
  Dihedral  :  5.773  34.231   1240
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.41 %
    Favored  : 86.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.34 (0.24), residues: 1148
  helix:  0.04 (0.28), residues: 341
  sheet: -2.95 (0.55), residues: 76
  loop : -3.52 (0.21), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1664 
 TYR   0.016   0.001   TYR A1486 
 PHE   0.019   0.002   PHE A1915 
 TRP   0.018   0.002   TRP A1689 
 HIS   0.004   0.001   HIS A1352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9379)
  covalent geometry    : angle       0.75623 (12718)
  hydrogen bonds       : bond        0.04160 (  268)
  hydrogen bonds       : angle       5.34902 (  771)
  metal coordination   : bond        0.01285 (    8)
  metal coordination   : angle      12.80182 (   12)

*********************** 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
  244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.311 
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: 0.6366 (t80) cc_final: 0.5871 (t80)
REVERT: B  214 LYS cc_start: 0.9366 (pttp) cc_final: 0.9078 (pttp)
REVERT: B  219 LEU cc_start: 0.9320 (mt) cc_final: 0.8970 (mt)
REVERT: B  289 ASN cc_start: 0.8982 (m110) cc_final: 0.7515 (t0)
REVERT: B  398 LYS cc_start: 0.8188 (pttt) cc_final: 0.7977 (ttmt)
REVERT: B  410 ASP cc_start: 0.8742 (m-30) cc_final: 0.7572 (t0)
REVERT: B  419 LYS cc_start: 0.9013 (mttt) cc_final: 0.8734 (mmmm)
REVERT: B  455 SER cc_start: 0.9408 (p) cc_final: 0.8925 (t)
REVERT: B  673 MET cc_start: 0.7873 (tpp) cc_final: 0.7638 (tpp)
REVERT: A 1439 MET cc_start: 0.8351 (pmm) cc_final: 0.7408 (pmm)
REVERT: A 1487 LEU cc_start: 0.9222 (tt) cc_final: 0.9007 (tt)
REVERT: A 1573 LEU cc_start: 0.9589 (tp) cc_final: 0.9298 (tp)
REVERT: A 1578 THR cc_start: 0.8713 (p) cc_final: 0.8249 (p)
REVERT: A 1860 TYR cc_start: 0.7577 (t80) cc_final: 0.7371 (t80)
REVERT: A 1910 ILE cc_start: 0.7727 (mt) cc_final: 0.7503 (mt)
REVERT: A 1912 MET cc_start: 0.5827 (ttm) cc_final: 0.5543 (ttm)
REVERT: A 1915 PHE cc_start: 0.6321 (p90) cc_final: 0.5956 (p90)
REVERT: A 1929 GLU cc_start: 0.8868 (tt0) cc_final: 0.8601 (mp0)
REVERT: A 2173 ASP cc_start: 0.8408 (p0) cc_final: 0.8166 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1045
  time to fit residues: 34.7726
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  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 104 optimal weight:    5.9990
   chunk 84 optimal weight:    0.6980
   chunk 17 optimal weight:   10.0000
   chunk 108 optimal weight:    8.9990
   chunk 117 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 340 HIS
B 474 ASN
A1326 GLN
A1364 GLN
** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.128197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.108345 restraints weight = 29843.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.110723 restraints weight = 21151.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.112398 restraints weight = 16269.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.113678 restraints weight = 13295.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.114575 restraints weight = 11351.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9387  Z= 0.252
  Angle     :  0.947  25.324  12730  Z= 0.448
  Chirality :  0.051   0.197   1486
  Planarity :  0.005   0.053   1606
  Dihedral  :  6.311  37.636   1240
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 18.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.94 %
    Favored  : 82.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.63 (0.23), residues: 1148
  helix: -0.32 (0.27), residues: 363
  sheet: -2.83 (0.51), residues: 98
  loop : -3.78 (0.21), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 180 
 TYR   0.019   0.002   TYR A1655 
 PHE   0.025   0.003   PHE B 192 
 TRP   0.023   0.003   TRP A1798 
 HIS   0.010   0.002   HIS A2168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 9379)
  covalent geometry    : angle       0.87377 (12718)
  hydrogen bonds       : bond        0.04638 (  268)
  hydrogen bonds       : angle       5.68596 (  771)
  metal coordination   : bond        0.01421 (    8)
  metal coordination   : angle      11.90297 (   12)

*********************** 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
  235 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.373 
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: B  183 TYR cc_start: 0.6280 (t80) cc_final: 0.5730 (t80)
REVERT: B  188 MET cc_start: 0.6915 (mtt) cc_final: 0.6308 (mtt)
REVERT: B  214 LYS cc_start: 0.9383 (pttp) cc_final: 0.9074 (pttp)
REVERT: B  217 MET cc_start: 0.8594 (ppp) cc_final: 0.8369 (ppp)
REVERT: B  219 LEU cc_start: 0.9318 (mt) cc_final: 0.9013 (mt)
REVERT: B  407 PHE cc_start: 0.8355 (m-80) cc_final: 0.7919 (m-80)
REVERT: B  419 LYS cc_start: 0.9068 (mttt) cc_final: 0.8748 (mmmm)
REVERT: B  455 SER cc_start: 0.9499 (p) cc_final: 0.9056 (t)
REVERT: B  641 LEU cc_start: 0.9039 (mt) cc_final: 0.8671 (mt)
REVERT: A 1353 ILE cc_start: 0.8064 (mm) cc_final: 0.7783 (tp)
REVERT: A 1439 MET cc_start: 0.8594 (pmm) cc_final: 0.7944 (pmm)
REVERT: A 1470 MET cc_start: 0.7565 (mtt) cc_final: 0.6919 (mtt)
REVERT: A 1474 GLU cc_start: 0.7404 (mp0) cc_final: 0.6793 (mp0)
REVERT: A 1570 TYR cc_start: 0.7872 (t80) cc_final: 0.7645 (t80)
REVERT: A 1915 PHE cc_start: 0.6775 (p90) cc_final: 0.6392 (p90)
REVERT: A 2173 ASP cc_start: 0.8390 (p0) cc_final: 0.8176 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1027
  time to fit residues: 33.1642
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  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 103 optimal weight:    0.1980
   chunk 91 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 114 optimal weight:    6.9990
   chunk 99 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    3.8388

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

Flipped N/Q/H residues before XYZ refinement:
A1326 GLN
A1364 GLN
** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2060 HIS
** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.128032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.108337 restraints weight = 29682.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.110667 restraints weight = 21108.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.112325 restraints weight = 16306.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.113425 restraints weight = 13388.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.114419 restraints weight = 11608.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.4800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9387  Z= 0.224
  Angle     :  0.931  22.867  12730  Z= 0.444
  Chirality :  0.050   0.196   1486
  Planarity :  0.005   0.052   1606
  Dihedral  :  6.483  38.146   1240
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 16.64 %
    Favored  : 83.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.56 (0.23), residues: 1148
  helix: -0.21 (0.27), residues: 354
  sheet: -2.73 (0.52), residues: 99
  loop : -3.73 (0.21), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1572 
 TYR   0.016   0.002   TYR A1486 
 PHE   0.023   0.002   PHE B 192 
 TRP   0.064   0.003   TRP A1689 
 HIS   0.011   0.002   HIS A2145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 9379)
  covalent geometry    : angle       0.86752 (12718)
  hydrogen bonds       : bond        0.04500 (  268)
  hydrogen bonds       : angle       5.73503 (  771)
  metal coordination   : bond        0.01391 (    8)
  metal coordination   : angle      11.07504 (   12)

*********************** 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
  236 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.382 
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  170 PHE cc_start: 0.8090 (t80) cc_final: 0.7734 (p90)
REVERT: B  183 TYR cc_start: 0.6459 (t80) cc_final: 0.5876 (t80)
REVERT: B  188 MET cc_start: 0.6880 (mtt) cc_final: 0.6335 (mtt)
REVERT: B  212 GLU cc_start: 0.8994 (pm20) cc_final: 0.8778 (pm20)
REVERT: B  214 LYS cc_start: 0.9370 (pttp) cc_final: 0.9053 (pttp)
REVERT: B  217 MET cc_start: 0.8529 (ppp) cc_final: 0.8274 (ppp)
REVERT: B  398 LYS cc_start: 0.8043 (pttm) cc_final: 0.7764 (ttmt)
REVERT: B  407 PHE cc_start: 0.8299 (m-80) cc_final: 0.7909 (m-80)
REVERT: B  419 LYS cc_start: 0.9033 (mttt) cc_final: 0.8746 (mmmm)
REVERT: B  455 SER cc_start: 0.9481 (p) cc_final: 0.9028 (t)
REVERT: B  673 MET cc_start: 0.7931 (tpp) cc_final: 0.7706 (tpp)
REVERT: A 1353 ILE cc_start: 0.8084 (mm) cc_final: 0.7866 (tp)
REVERT: A 1439 MET cc_start: 0.8631 (pmm) cc_final: 0.7898 (pmm)
REVERT: A 1470 MET cc_start: 0.7950 (mtt) cc_final: 0.7702 (mtt)
REVERT: A 1474 GLU cc_start: 0.7388 (mp0) cc_final: 0.6761 (mp0)
REVERT: A 1570 TYR cc_start: 0.7908 (t80) cc_final: 0.7606 (t80)
REVERT: A 1614 LYS cc_start: 0.4407 (tmtt) cc_final: 0.3330 (tttt)
REVERT: A 1910 ILE cc_start: 0.7866 (mt) cc_final: 0.7544 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1020
  time to fit residues: 33.2309
Evaluate side-chains
  183 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0570
   chunk 66 optimal weight:    0.0670
   chunk 12 optimal weight:   10.0000
   chunk 89 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   overall best weight:    0.5236

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

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN
B 474 ASN
B 517 ASN
A1326 GLN
A1373 ASN
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1703 ASN ** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.135240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.114110 restraints weight = 28957.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.116622 restraints weight = 20772.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.118412 restraints weight = 16047.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.119666 restraints weight = 13161.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.120685 restraints weight = 11321.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.5146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9387  Z= 0.139
  Angle     :  0.841  19.322  12730  Z= 0.404
  Chirality :  0.049   0.230   1486
  Planarity :  0.004   0.050   1606
  Dihedral  :  6.025  35.944   1240
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.24 %
    Favored  : 86.76 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.61 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.11 (0.24), residues: 1148
  helix:  0.26 (0.28), residues: 353
  sheet: -1.90 (0.58), residues: 88
  loop : -3.59 (0.21), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1572 
 TYR   0.023   0.001   TYR A1879 
 PHE   0.042   0.002   PHE A1828 
 TRP   0.039   0.002   TRP A1689 
 HIS   0.006   0.001   HIS A2145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9379)
  covalent geometry    : angle       0.80537 (12718)
  hydrogen bonds       : bond        0.03808 (  268)
  hydrogen bonds       : angle       5.31329 (  771)
  metal coordination   : bond        0.01061 (    8)
  metal coordination   : angle       7.95369 (   12)

*********************** 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
  236 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.478 
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: B  170 PHE cc_start: 0.7937 (t80) cc_final: 0.7709 (p90)
REVERT: B  180 ARG cc_start: 0.6551 (tpp-160) cc_final: 0.6323 (tpp-160)
REVERT: B  183 TYR cc_start: 0.6630 (t80) cc_final: 0.6094 (t80)
REVERT: B  188 MET cc_start: 0.6640 (mtt) cc_final: 0.6085 (mtt)
REVERT: B  212 GLU cc_start: 0.9030 (pm20) cc_final: 0.8574 (pm20)
REVERT: B  214 LYS cc_start: 0.9170 (pttp) cc_final: 0.8807 (pttp)
REVERT: B  219 LEU cc_start: 0.9273 (mt) cc_final: 0.8946 (mt)
REVERT: B  223 TYR cc_start: 0.8472 (m-10) cc_final: 0.7832 (m-10)
REVERT: B  226 ASN cc_start: 0.9046 (t0) cc_final: 0.8798 (t0)
REVERT: B  230 MET cc_start: 0.9053 (mmp) cc_final: 0.8759 (mmm)
REVERT: B  398 LYS cc_start: 0.8073 (pttm) cc_final: 0.7543 (ttmt)
REVERT: B  419 LYS cc_start: 0.8912 (mttt) cc_final: 0.8632 (mmmm)
REVERT: B  455 SER cc_start: 0.9380 (p) cc_final: 0.8894 (t)
REVERT: B  627 ASP cc_start: 0.8386 (t0) cc_final: 0.8109 (t0)
REVERT: B  636 PRO cc_start: 0.8481 (Cg_endo) cc_final: 0.8264 (Cg_exo)
REVERT: B  641 LEU cc_start: 0.8965 (mt) cc_final: 0.7745 (mt)
REVERT: B  673 MET cc_start: 0.7857 (tpp) cc_final: 0.7596 (tpp)
REVERT: A 1439 MET cc_start: 0.8452 (pmm) cc_final: 0.7407 (pmm)
REVERT: A 1470 MET cc_start: 0.7977 (mtt) cc_final: 0.7372 (mtt)
REVERT: A 1570 TYR cc_start: 0.7952 (t80) cc_final: 0.7676 (t80)
REVERT: A 1614 LYS cc_start: 0.3476 (tmtt) cc_final: 0.2589 (tttt)
REVERT: A 1794 MET cc_start: 0.8471 (mmt) cc_final: 0.8186 (mmt)
REVERT: A 1798 TRP cc_start: 0.7803 (m-10) cc_final: 0.7522 (m-10)
REVERT: A 1876 GLU cc_start: 0.8953 (tt0) cc_final: 0.8579 (tt0)
REVERT: A 1899 ASP cc_start: 0.7459 (t70) cc_final: 0.7097 (t0)
REVERT: A 1910 ILE cc_start: 0.7437 (mt) cc_final: 0.7208 (mt)
REVERT: A 1915 PHE cc_start: 0.6837 (p90) cc_final: 0.6292 (p90)
REVERT: A 1920 LEU cc_start: 0.7690 (pp) cc_final: 0.7397 (pp)
REVERT: A 2062 MET cc_start: 0.6810 (pmm) cc_final: 0.6385 (mpp)
  outliers start: 1
  outliers final: 1
  residues processed: 236
  average time/residue: 0.0942
  time to fit residues: 31.3980
Evaluate side-chains
  198 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 3 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 28 optimal weight:    0.3980
   chunk 93 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN
B 517 ASN
A1326 GLN
** A1587 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.133523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.112406 restraints weight = 29202.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.114920 restraints weight = 20656.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.116723 restraints weight = 15913.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.118107 restraints weight = 13049.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.119127 restraints weight = 11159.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.5303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9387  Z= 0.155
  Angle     :  0.838  17.065  12730  Z= 0.409
  Chirality :  0.050   0.263   1486
  Planarity :  0.005   0.078   1606
  Dihedral  :  5.964  37.616   1240
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.02 %
    Favored  : 85.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.93 (0.24), residues: 1148
  helix:  0.51 (0.28), residues: 341
  sheet: -1.29 (0.58), residues: 95
  loop : -3.57 (0.21), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 352 
 TYR   0.014   0.001   TYR A1486 
 PHE   0.036   0.002   PHE A1828 
 TRP   0.035   0.002   TRP A1689 
 HIS   0.006   0.001   HIS A2145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9379)
  covalent geometry    : angle       0.81227 (12718)
  hydrogen bonds       : bond        0.03853 (  268)
  hydrogen bonds       : angle       5.31023 (  771)
  metal coordination   : bond        0.01262 (    8)
  metal coordination   : angle       6.76250 (   12)

*********************** 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
  224 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.451 
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  180 ARG cc_start: 0.6698 (tpp-160) cc_final: 0.6239 (tpp80)
REVERT: B  183 TYR cc_start: 0.6648 (t80) cc_final: 0.6180 (t80)
REVERT: B  188 MET cc_start: 0.6709 (mtt) cc_final: 0.6121 (mtt)
REVERT: B  214 LYS cc_start: 0.9223 (pttp) cc_final: 0.8873 (pttp)
REVERT: B  219 LEU cc_start: 0.9297 (mt) cc_final: 0.8964 (mt)
REVERT: B  223 TYR cc_start: 0.8553 (m-10) cc_final: 0.7874 (m-10)
REVERT: B  289 ASN cc_start: 0.8951 (m110) cc_final: 0.7648 (t0)
REVERT: B  398 LYS cc_start: 0.8032 (pttm) cc_final: 0.7640 (ttmt)
REVERT: B  414 MET cc_start: 0.8742 (mpp) cc_final: 0.8525 (mpp)
REVERT: B  417 LEU cc_start: 0.9263 (mp) cc_final: 0.8973 (mt)
REVERT: B  673 MET cc_start: 0.7897 (tpp) cc_final: 0.7652 (tpp)
REVERT: A 1337 GLU cc_start: 0.8466 (tp30) cc_final: 0.8197 (tp30)
REVERT: A 1439 MET cc_start: 0.8479 (pmm) cc_final: 0.7534 (pmm)
REVERT: A 1470 MET cc_start: 0.8087 (mtt) cc_final: 0.7596 (mtt)
REVERT: A 1474 GLU cc_start: 0.7108 (mp0) cc_final: 0.6541 (mp0)
REVERT: A 1570 TYR cc_start: 0.7918 (t80) cc_final: 0.7710 (t80)
REVERT: A 1614 LYS cc_start: 0.3014 (tmtt) cc_final: 0.2173 (tttt)
REVERT: A 1794 MET cc_start: 0.8441 (mmt) cc_final: 0.7812 (mmm)
REVERT: A 1827 LEU cc_start: 0.7719 (tt) cc_final: 0.7395 (mm)
REVERT: A 1876 GLU cc_start: 0.8922 (tt0) cc_final: 0.8588 (tt0)
REVERT: A 1899 ASP cc_start: 0.7522 (t70) cc_final: 0.7139 (t0)
REVERT: A 1915 PHE cc_start: 0.7024 (p90) cc_final: 0.6380 (p90)
REVERT: A 2062 MET cc_start: 0.6896 (pmm) cc_final: 0.6457 (mpp)
REVERT: A 2144 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6897 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.0924
  time to fit residues: 29.4282
Evaluate side-chains
  187 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0040
   chunk 91 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 115 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
A1326 GLN
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1703 ASN ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.136506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.115172 restraints weight = 28868.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.117727 restraints weight = 20516.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.119567 restraints weight = 15824.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.120959 restraints weight = 12984.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.121962 restraints weight = 11118.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.5531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9387  Z= 0.132
  Angle     :  0.812  13.675  12730  Z= 0.393
  Chirality :  0.049   0.238   1486
  Planarity :  0.005   0.057   1606
  Dihedral  :  5.802  36.986   1240
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.89 %
    Favored  : 87.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.77 (0.25), residues: 1148
  helix:  0.67 (0.29), residues: 342
  sheet: -1.40 (0.63), residues: 85
  loop : -3.44 (0.21), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 352 
 TYR   0.016   0.001   TYR B 672 
 PHE   0.024   0.002   PHE B 170 
 TRP   0.043   0.002   TRP A1906 
 HIS   0.005   0.001   HIS A2145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9379)
  covalent geometry    : angle       0.79346 (12718)
  hydrogen bonds       : bond        0.03584 (  268)
  hydrogen bonds       : angle       5.13184 (  771)
  metal coordination   : bond        0.01048 (    8)
  metal coordination   : angle       5.67484 (   12)

*********************** 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
  235 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.444 
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: 0.6969 (tpp-160) cc_final: 0.6471 (tpp80)
REVERT: B  183 TYR cc_start: 0.6487 (t80) cc_final: 0.5990 (t80)
REVERT: B  188 MET cc_start: 0.6577 (mtt) cc_final: 0.6006 (mtt)
REVERT: B  212 GLU cc_start: 0.8981 (pm20) cc_final: 0.8494 (pm20)
REVERT: B  213 ASP cc_start: 0.9359 (m-30) cc_final: 0.9145 (m-30)
REVERT: B  219 LEU cc_start: 0.9176 (mt) cc_final: 0.8831 (mt)
REVERT: B  223 TYR cc_start: 0.8527 (m-10) cc_final: 0.7845 (m-10)
REVERT: B  226 ASN cc_start: 0.9063 (t0) cc_final: 0.8789 (t0)
REVERT: B  230 MET cc_start: 0.9068 (mmp) cc_final: 0.8765 (mmm)
REVERT: B  289 ASN cc_start: 0.8876 (m110) cc_final: 0.7623 (t0)
REVERT: B  398 LYS cc_start: 0.8112 (pttm) cc_final: 0.7575 (ttmt)
REVERT: B  462 PHE cc_start: 0.8786 (m-80) cc_final: 0.8517 (m-80)
REVERT: B  627 ASP cc_start: 0.8243 (t0) cc_final: 0.7936 (t0)
REVERT: B  673 MET cc_start: 0.7912 (tpp) cc_final: 0.7701 (tpp)
REVERT: A 1337 GLU cc_start: 0.8420 (tp30) cc_final: 0.8193 (tp30)
REVERT: A 1439 MET cc_start: 0.8429 (pmm) cc_final: 0.7469 (pmm)
REVERT: A 1470 MET cc_start: 0.8121 (mtt) cc_final: 0.7732 (mtt)
REVERT: A 1474 GLU cc_start: 0.6950 (mp0) cc_final: 0.6348 (mp0)
REVERT: A 1575 GLN cc_start: 0.9607 (mt0) cc_final: 0.9203 (mt0)
REVERT: A 1614 LYS cc_start: 0.3023 (tmtt) cc_final: 0.2131 (tttt)
REVERT: A 1794 MET cc_start: 0.8437 (mmt) cc_final: 0.8158 (mmm)
REVERT: A 1798 TRP cc_start: 0.7684 (m-10) cc_final: 0.7361 (m-10)
REVERT: A 1876 GLU cc_start: 0.8789 (tt0) cc_final: 0.8452 (tt0)
REVERT: A 1899 ASP cc_start: 0.7376 (t70) cc_final: 0.7050 (t0)
REVERT: A 1920 LEU cc_start: 0.7956 (pp) cc_final: 0.7624 (pp)
REVERT: A 2062 MET cc_start: 0.6814 (pmm) cc_final: 0.6302 (mpp)
REVERT: A 2144 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6785 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0933
  time to fit residues: 31.0940
Evaluate side-chains
  198 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 102 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0870
   chunk 35 optimal weight:    0.0050
   chunk 106 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0370
   chunk 72 optimal weight:    0.0070
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.2270

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

Flipped N/Q/H residues before XYZ refinement:
A1326 GLN
A1373 ASN
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1662 ASN
** A1703 ASN ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.139151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.116745 restraints weight = 28404.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.119461 restraints weight = 19824.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.121452 restraints weight = 15182.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.122906 restraints weight = 12384.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.123991 restraints weight = 10589.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.5844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9387  Z= 0.132
  Angle     :  0.801  10.475  12730  Z= 0.388
  Chirality :  0.049   0.212   1486
  Planarity :  0.005   0.057   1606
  Dihedral  :  5.656  37.270   1240
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.02 %
    Favored  : 87.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.36 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.64 (0.25), residues: 1148
  helix:  0.80 (0.29), residues: 344
  sheet: -1.31 (0.61), residues: 85
  loop : -3.37 (0.21), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A2166 
 TYR   0.029   0.001   TYR A1879 
 PHE   0.022   0.002   PHE B 170 
 TRP   0.048   0.002   TRP A1906 
 HIS   0.004   0.001   HIS A2145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9379)
  covalent geometry    : angle       0.79027 (12718)
  hydrogen bonds       : bond        0.03354 (  268)
  hydrogen bonds       : angle       4.98884 (  771)
  metal coordination   : bond        0.00838 (    8)
  metal coordination   : angle       4.39698 (   12)

********************** 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
  232 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.367 
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: 0.7075 (tpp-160) cc_final: 0.6556 (tpp80)
REVERT: B  181 PHE cc_start: 0.7627 (m-10) cc_final: 0.7407 (m-10)
REVERT: B  183 TYR cc_start: 0.6532 (t80) cc_final: 0.6073 (t80)
REVERT: B  188 MET cc_start: 0.6483 (mtt) cc_final: 0.5884 (mtt)
REVERT: B  214 LYS cc_start: 0.9294 (pttp) cc_final: 0.8991 (pttm)
REVERT: B  217 MET cc_start: 0.8356 (ppp) cc_final: 0.7841 (ppp)
REVERT: B  219 LEU cc_start: 0.9229 (mt) cc_final: 0.8913 (mt)
REVERT: B  223 TYR cc_start: 0.8502 (m-10) cc_final: 0.7915 (m-10)
REVERT: B  289 ASN cc_start: 0.8787 (m110) cc_final: 0.7578 (t0)
REVERT: B  398 LYS cc_start: 0.8094 (pttm) cc_final: 0.7662 (ttmt)
REVERT: B  414 MET cc_start: 0.8788 (mpp) cc_final: 0.8440 (mpp)
REVERT: B  422 GLN cc_start: 0.9061 (tt0) cc_final: 0.8263 (mm110)
REVERT: B  462 PHE cc_start: 0.8784 (m-80) cc_final: 0.8481 (m-80)
REVERT: B  627 ASP cc_start: 0.8259 (t0) cc_final: 0.7687 (t0)
REVERT: B  631 THR cc_start: 0.7960 (m) cc_final: 0.6135 (m)
REVERT: B  673 MET cc_start: 0.7933 (tpp) cc_final: 0.7713 (tpp)
REVERT: A 1337 GLU cc_start: 0.8303 (tp30) cc_final: 0.8075 (tp30)
REVERT: A 1439 MET cc_start: 0.8487 (pmm) cc_final: 0.7739 (pmm)
REVERT: A 1470 MET cc_start: 0.8448 (mtt) cc_final: 0.8100 (mtt)
REVERT: A 1570 TYR cc_start: 0.8140 (t80) cc_final: 0.7876 (t80)
REVERT: A 1575 GLN cc_start: 0.9600 (mt0) cc_final: 0.9254 (mt0)
REVERT: A 1614 LYS cc_start: 0.2758 (tmtt) cc_final: 0.1954 (tttt)
REVERT: A 1798 TRP cc_start: 0.7773 (m-10) cc_final: 0.7486 (m-10)
REVERT: A 1876 GLU cc_start: 0.8583 (tt0) cc_final: 0.8213 (tt0)
REVERT: A 1899 ASP cc_start: 0.7303 (t70) cc_final: 0.6856 (t0)
REVERT: A 1915 PHE cc_start: 0.6733 (p90) cc_final: 0.6417 (p90)
REVERT: A 2062 MET cc_start: 0.6790 (pmm) cc_final: 0.6212 (mpp)
REVERT: A 2144 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6783 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.0889
  time to fit residues: 29.2602
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  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 100 optimal weight:   50.0000
   chunk 65 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 73 optimal weight:    0.4980
   chunk 94 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN
B 517 ASN
A1326 GLN
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1703 ASN ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.137510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.116017 restraints weight = 28263.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.118550 restraints weight = 20148.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.120340 restraints weight = 15618.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.121708 restraints weight = 12878.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.122675 restraints weight = 11074.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.5871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9387  Z= 0.131
  Angle     :  0.812  10.733  12730  Z= 0.393
  Chirality :  0.048   0.292   1486
  Planarity :  0.005   0.050   1606
  Dihedral  :  5.667  38.136   1240
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.85 %
    Favored  : 88.15 %
  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 : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.49 (0.25), residues: 1148
  helix:  0.93 (0.29), residues: 346
  sheet: -1.27 (0.63), residues: 82
  loop : -3.29 (0.22), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A2166 
 TYR   0.015   0.001   TYR B 672 
 PHE   0.020   0.002   PHE A1915 
 TRP   0.040   0.002   TRP A1906 
 HIS   0.004   0.001   HIS A2145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9379)
  covalent geometry    : angle       0.80038 (12718)
  hydrogen bonds       : bond        0.03401 (  268)
  hydrogen bonds       : angle       5.01405 (  771)
  metal coordination   : bond        0.00906 (    8)
  metal coordination   : angle       4.51514 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1647.95 seconds
wall clock time: 29 minutes 15.99 seconds (1755.99 seconds total)