Starting phenix.real_space_refine
on Wed Mar  4 05:52:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kvf_23049/03_2026/7kvf_23049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kvf_23049/03_2026/7kvf_23049.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kvf_23049/03_2026/7kvf_23049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kvf_23049/03_2026/7kvf_23049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kvf_23049/03_2026/7kvf_23049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kvf_23049/03_2026/7kvf_23049.cif"
  }
  resolution = 3.6
  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=   0.000 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    7074      2.51       5
     N    1905      2.21       5
     O    2108      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11142
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 11142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1374, 11142
          Classifications: {'peptide': 1374}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 66, 'TRANS': 1305}
          Chain breaks: 1
  Time building chain proxies: 2.70, per 1000 atoms: 0.24
  Number of scatterers: 11142
  At special positions: 0
  Unit cell: (100.1, 106.7, 141.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    2108      8.00
     N    1905      7.00
     C    7074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 139 " - pdb=" SG  CYS B 165 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 220 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 472 " - pdb=" SG  CYS B 498 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1697 " - pdb=" SG  CYS B1723 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1879 " - pdb=" SG  CYS B2033 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B2038 " - pdb=" SG  CYS B2193 " distance=2.04

  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: 0.96
  Conformation dependent library (CDL) restraints added in 674.6 milliseconds
  

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2588

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 21 sheets defined
      6.8% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'B' and resid 23 through 28
      removed outlier: 4.475A  pdb=" N   LEU B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
      removed outlier: 3.904A  pdb=" N   LYS B  46 " --> pdb=" O   PRO B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 195
    Processing helix  chain 'B' and resid 344 through 352
      removed outlier: 3.948A  pdb=" N   ARG B 348 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   SER B 349 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 490
    Processing helix  chain 'B' and resid 526 through 528
      No H-bonds generated for 'chain 'B' and resid 526 through 528'
    Processing helix  chain 'B' and resid 549 through 556
      removed outlier: 3.779A  pdb=" N   ASN B 556 " --> pdb=" O   PHE B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1608 through 1612
      removed outlier: 4.352A  pdb=" N   HIS B1612 " --> pdb=" O   TYR B1609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1650 through 1654
      removed outlier: 3.612A  pdb=" N   GLU B1654 " --> pdb=" O   LYS B1651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1665 through 1669
      removed outlier: 3.606A  pdb=" N   GLU B1668 " --> pdb=" O   TRP B1665 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ASP B1669 " --> pdb=" O   PHE B1666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1665 through 1669'
    Processing helix  chain 'B' and resid 1685 through 1689
    Processing helix  chain 'B' and resid 1707 through 1713
      removed outlier: 3.863A  pdb=" N   ILE B1712 " --> pdb=" O   PRO B1708 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   HIS B1713 " --> pdb=" O   GLU B1709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1768 through 1772
      removed outlier: 4.038A  pdb=" N   LYS B1772 " --> pdb=" O   SER B1769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1860 through 1865
      removed outlier: 3.833A  pdb=" N   ARG B1865 " --> pdb=" O   GLY B1861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1891 through 1893
      No H-bonds generated for 'chain 'B' and resid 1891 through 1893'
    Processing helix  chain 'B' and resid 1905 through 1909
    Processing helix  chain 'B' and resid 2050 through 2052
      No H-bonds generated for 'chain 'B' and resid 2050 through 2052'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 40
      removed outlier: 3.670A  pdb=" N   GLN B  11 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   ARG B   4 " --> pdb=" O   LYS B  71 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   HIS B  73 " --> pdb=" O   ARG B   4 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   PHE B   6 " --> pdb=" O   HIS B  73 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE B  70 " --> pdb=" O   TRP B 124 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 64
      removed outlier: 6.768A  pdb=" N   LEU B  62 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 76
      removed outlier: 3.519A  pdb=" N   ASN B  76 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ARG B 118 " --> pdb=" O   ASN B  76 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 189
      removed outlier: 6.339A  pdb=" N   LEU B 185 " --> pdb=" O   LEU B 230 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   MET B 232 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   PHE B 187 " --> pdb=" O   MET B 232 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   MET B 270 " --> pdb=" O   ILE B 225 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA B 268 " --> pdb=" O   TRP B 227 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 217 through 219
      removed outlier: 3.521A  pdb=" N   ILE B 217 " --> pdb=" O   TYR B 295 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 371
      removed outlier: 4.167A  pdb=" N   PHE B 325 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   TYR B 324 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   LYS B 408 " --> pdb=" O   TYR B 324 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ILE B 326 " --> pdb=" O   LYS B 408 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE B 407 " --> pdb=" O   TYR B 453 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 397
    Processing sheet with id=AA8, first strand: chain 'B' and resid 515 through 520
      removed outlier: 3.695A  pdb=" N   CYS B 585 " --> pdb=" O   ALA B 518 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 522 through 524
    Processing sheet with id=AB1, first strand: chain 'B' and resid 612 through 615
      removed outlier: 3.815A  pdb=" N   LEU B 613 " --> pdb=" O   ILE B 596 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU B 594 " --> pdb=" O   LEU B 615 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1550 through 1554
      removed outlier: 5.491A  pdb=" N   ASN B1550 " --> pdb=" O   VAL B1627 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   GLN B1629 " --> pdb=" O   ASN B1550 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ARG B1552 " --> pdb=" O   GLN B1629 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   ARG B1631 " --> pdb=" O   ARG B1552 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   TYR B1554 " --> pdb=" O   ARG B1631 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1556 through 1563
      removed outlier: 3.907A  pdb=" N   ALA B1557 " --> pdb=" O   ARG B1593 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG B1593 " --> pdb=" O   ALA B1557 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 1697 through 1698
    Processing sheet with id=AB5, first strand: chain 'B' and resid 1701 through 1703
    Processing sheet with id=AB6, first strand: chain 'B' and resid 1776 through 1780
      removed outlier: 3.513A  pdb=" N   MET B1746 " --> pdb=" O   ALA B1779 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1791 through 1792
    Processing sheet with id=AB8, first strand: chain 'B' and resid 1834 through 1836
    Processing sheet with id=AB9, first strand: chain 'B' and resid 1881 through 1882
      removed outlier: 6.390A  pdb=" N   GLN B2031 " --> pdb=" O   THR B1946 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL B1943 " --> pdb=" O   ALA B2010 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   GLY B1947 " --> pdb=" O   PRO B2006 " (cutoff:3.500A)
      removed outlier: 11.882A  pdb=" N   GLN B1949 " --> pdb=" O   PHE B2004 " (cutoff:3.500A)
      removed outlier: 12.332A  pdb=" N   PHE B2004 " --> pdb=" O   GLN B1949 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 1895 through 1897
      removed outlier: 6.746A  pdb=" N   GLU B1964 " --> pdb=" O   THR B2018 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ALA B2020 " --> pdb=" O   THR B1962 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   THR B1962 " --> pdb=" O   ALA B2020 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 2040 through 2041
      removed outlier: 3.788A  pdb=" N   THR B2040 " --> pdb=" O   GLY B2192 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY B2192 " --> pdb=" O   THR B2040 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   GLU B2189 " --> pdb=" O   ILE B2108 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   ILE B2108 " --> pdb=" O   GLU B2189 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   PHE B2191 " --> pdb=" O   THR B2106 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ARG B2171 " --> pdb=" O   LEU B2099 " (cutoff:3.500A)
      removed outlier: 10.342A  pdb=" N   LYS B2101 " --> pdb=" O   ILE B2169 " (cutoff:3.500A)
      removed outlier: 9.333A  pdb=" N   ILE B2169 " --> pdb=" O   LYS B2101 " (cutoff:3.500A)
      removed outlier: 9.659A  pdb=" N   LYS B2103 " --> pdb=" O   PRO B2167 " (cutoff:3.500A)
      removed outlier: 10.470A  pdb=" N   ILE B2105 " --> pdb=" O   ASN B2165 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   ASN B2165 " --> pdb=" O   ILE B2105 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ALA B2107 " --> pdb=" O   PHE B2163 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   PHE B2163 " --> pdb=" O   ALA B2107 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ILE B2109 " --> pdb=" O   LYS B2161 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   LYS B2161 " --> pdb=" O   ILE B2109 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   SER B2124 " --> pdb=" O   LYS B2178 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   TRP B2180 " --> pdb=" O   VAL B2122 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL B2122 " --> pdb=" O   TRP B2180 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   MET B2120 " --> pdb=" O   CYS B2113 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   CYS B2113 " --> pdb=" O   MET B2120 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 2054 through 2056
      removed outlier: 6.999A  pdb=" N   ARG B2171 " --> pdb=" O   LEU B2099 " (cutoff:3.500A)
      removed outlier: 10.342A  pdb=" N   LYS B2101 " --> pdb=" O   ILE B2169 " (cutoff:3.500A)
      removed outlier: 9.333A  pdb=" N   ILE B2169 " --> pdb=" O   LYS B2101 " (cutoff:3.500A)
      removed outlier: 9.659A  pdb=" N   LYS B2103 " --> pdb=" O   PRO B2167 " (cutoff:3.500A)
      removed outlier: 10.470A  pdb=" N   ILE B2105 " --> pdb=" O   ASN B2165 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   ASN B2165 " --> pdb=" O   ILE B2105 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ALA B2107 " --> pdb=" O   PHE B2163 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   PHE B2163 " --> pdb=" O   ALA B2107 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ILE B2109 " --> pdb=" O   LYS B2161 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   LYS B2161 " --> pdb=" O   ILE B2109 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   SER B2124 " --> pdb=" O   LYS B2178 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   TRP B2180 " --> pdb=" O   VAL B2122 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL B2122 " --> pdb=" O   TRP B2180 " (cutoff:3.500A)

    160 hydrogen bonds defined for protein.
    384 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.32

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1844
        1.29 -     1.42: 3119
        1.42 -     1.56: 6380
        1.56 -     1.70: 1
        1.70 -     1.83: 92
  Bond restraints: 11436
  Sorted by residual:
  bond pdb=" C   VAL B 654 "
       pdb=" O   VAL B 654 "
    ideal  model  delta    sigma   weight residual
    1.231  1.153  0.078 1.29e-02 6.01e+03 3.63e+01
  bond pdb=" C   CYS B 656 "
       pdb=" O   CYS B 656 "
    ideal  model  delta    sigma   weight residual
    1.235  1.188  0.047 1.26e-02 6.30e+03 1.38e+01
  bond pdb=" C   ASP B 653 "
       pdb=" N   VAL B 654 "
    ideal  model  delta    sigma   weight residual
    1.331  1.290  0.041 1.20e-02 6.94e+03 1.19e+01
  bond pdb=" C   ASN B 541 "
       pdb=" N   PRO B 542 "
    ideal  model  delta    sigma   weight residual
    1.331  1.359 -0.027 7.90e-03 1.60e+04 1.18e+01
  bond pdb=" CA  VAL B 654 "
       pdb=" C   VAL B 654 "
    ideal  model  delta    sigma   weight residual
    1.526  1.477  0.049 1.43e-02 4.89e+03 1.16e+01
  ... (remaining 11431 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 15170
        2.42 -     4.84: 283
        4.84 -     7.25: 25
        7.25 -     9.67: 9
        9.67 -    12.09: 3
  Bond angle restraints: 15490
  Sorted by residual:
  angle pdb=" N   VAL B 654 "
        pdb=" CA  VAL B 654 "
        pdb=" CB  VAL B 654 "
      ideal   model   delta    sigma   weight residual
     112.60  100.51   12.09 1.29e+00 6.01e-01 8.78e+01
  angle pdb=" N   PHE B2059 "
        pdb=" CA  PHE B2059 "
        pdb=" C   PHE B2059 "
      ideal   model   delta    sigma   weight residual
     112.72  103.01    9.71 1.36e+00 5.41e-01 5.10e+01
  angle pdb=" N   VAL B1706 "
        pdb=" CA  VAL B1706 "
        pdb=" C   VAL B1706 "
      ideal   model   delta    sigma   weight residual
     112.12  107.30    4.82 8.40e-01 1.42e+00 3.29e+01
  angle pdb=" N   ASP B 401 "
        pdb=" CA  ASP B 401 "
        pdb=" C   ASP B 401 "
      ideal   model   delta    sigma   weight residual
     112.57  106.64    5.93 1.13e+00 7.83e-01 2.75e+01
  angle pdb=" C   ASN B2036 "
        pdb=" N   GLY B2037 "
        pdb=" CA  GLY B2037 "
      ideal   model   delta    sigma   weight residual
     121.51  129.34   -7.83 1.52e+00 4.33e-01 2.65e+01
  ... (remaining 15485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 6070
       17.94 -    35.88: 666
       35.88 -    53.82: 92
       53.82 -    71.76: 20
       71.76 -    89.70: 8
  Dihedral angle restraints: 6856
    sinusoidal: 2828
      harmonic: 4028
  Sorted by residual:
  dihedral pdb=" CB  CYS B 139 "
           pdb=" SG  CYS B 139 "
           pdb=" SG  CYS B 165 "
           pdb=" CB  CYS B 165 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   20.33   72.67     1      1.00e+01 1.00e-02 6.74e+01
  dihedral pdb=" N   VAL B 654 "
           pdb=" C   VAL B 654 "
           pdb=" CA  VAL B 654 "
           pdb=" CB  VAL B 654 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  108.17   15.23     0      2.50e+00 1.60e-01 3.71e+01
  dihedral pdb=" CA  ARG B  90 "
           pdb=" C   ARG B  90 "
           pdb=" N   TYR B  91 "
           pdb=" CA  TYR B  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.50  -24.50     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 6853 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 1519
       0.100 -    0.199: 101
       0.199 -    0.299: 3
       0.299 -    0.398: 3
       0.398 -    0.498: 1
  Chirality restraints: 1627
  Sorted by residual:
  chirality pdb=" CB  VAL B 654 "
            pdb=" CA  VAL B 654 "
            pdb=" CG1 VAL B 654 "
            pdb=" CG2 VAL B 654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.13   -0.50 2.00e-01 2.50e+01 6.19e+00
  chirality pdb=" CA  ASP B 660 "
            pdb=" N   ASP B 660 "
            pdb=" C   ASP B 660 "
            pdb=" CB  ASP B 660 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.28e+00
  chirality pdb=" CA  VAL B 654 "
            pdb=" N   VAL B 654 "
            pdb=" C   VAL B 654 "
            pdb=" CB  VAL B 654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.79   -0.35 2.00e-01 2.50e+01 2.99e+00
  ... (remaining 1624 not shown)

  Planarity restraints: 1999
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B2033 "   -0.021 2.00e-02 2.50e+03   4.13e-02 1.71e+01
        pdb=" C   CYS B2033 "    0.071 2.00e-02 2.50e+03
        pdb=" O   CYS B2033 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLU B2034 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 669 "    0.060 5.00e-02 4.00e+02   9.13e-02 1.33e+01
        pdb=" N   PRO B 670 "   -0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO B 670 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 670 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B2023 "   -0.033 5.00e-02 4.00e+02   4.94e-02 3.91e+00
        pdb=" N   PRO B2024 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B2024 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B2024 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1996 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1223
        2.74 -     3.28: 11124
        3.28 -     3.82: 17231
        3.82 -     4.36: 20716
        4.36 -     4.90: 36116
  Nonbonded interactions: 86410
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 191 "
            pdb=" OG  SER B 193 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OH  TYR B1609 "
            pdb=" OD2 ASP B2005 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   SER B 349 "
            pdb=" NE2 GLN B 358 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OH  TYR B1554 "
            pdb=" O   ARG B1621 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OH  TYR B 605 "
            pdb=" OE2 GLU B 621 "
     model   vdw
     2.214 3.040
  ... (remaining 86405 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.100
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
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      :  0.005   0.078  11442  Z= 0.257
  Angle     :  0.818  12.087  15502  Z= 0.482
  Chirality :  0.053   0.498   1627
  Planarity :  0.005   0.091   1999
  Dihedral  : 14.673  89.697   4250
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 17.14
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 18.25 %
    Favored  : 81.39 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.65 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -5.88 (0.17), residues: 1370
  helix: -4.25 (0.41), residues: 45
  sheet: -3.39 (0.23), residues: 373
  loop : -4.44 (0.14), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  90 
 TYR   0.021   0.002   TYR B 363 
 PHE   0.016   0.001   PHE B2071 
 TRP   0.025   0.002   TRP B1700 
 HIS   0.005   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (11436)
  covalent geometry    : angle       0.81660 (15490)
  SS BOND              : bond        0.00789 (    6)
  SS BOND              : angle       1.65774 (   12)
  hydrogen bonds       : bond        0.29500 (  150)
  hydrogen bonds       : angle      12.46977 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 178
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  343 MET cc_start: -0.0768 (tpt) cc_final: -0.2783 (tmm)
REVERT: B  491 LEU cc_start: 0.5908 (mt) cc_final: 0.5376 (mt)
REVERT: B  613 LEU cc_start: 0.8120 (tp) cc_final: 0.7800 (tt)
REVERT: B  619 ARG cc_start: 0.8250 (ptt90) cc_final: 0.7877 (tpp-160)
  outliers start: 7
  outliers final: 2
  residues processed: 184
  average time/residue: 0.1137
  time to fit residues: 29.3888
Evaluate side-chains
  122 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1750 GLU
Chi-restraints excluded: chain B residue 2061 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
** B  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  87 GLN
B 134 HIS
B 182 GLN
B 222 HIS
B 307 ASN
B 315 GLN
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 362 HIS
B 556 ASN
B 562 ASN
B 583 HIS
B 609 HIS
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 700 ASN
** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1643 HIS
B1645 HIS
B1670 ASN
B1713 HIS
** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1819 GLN
B1828 GLN
B1830 GLN
B2002 ASN
B2046 ASN
B2093 GLN
B2128 HIS
B2162 ASN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.077226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.059168 restraints weight = 62505.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.060497 restraints weight = 45733.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.061396 restraints weight = 37005.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.062056 restraints weight = 32031.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.062310 restraints weight = 28904.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  11442  Z= 0.250
  Angle     :  0.795  10.869  15502  Z= 0.413
  Chirality :  0.047   0.197   1627
  Planarity :  0.006   0.094   1999
  Dihedral  :  6.720  45.518   1515
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.45 %
    Favored  : 85.55 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.18 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -5.27 (0.18), residues: 1370
  helix: -3.49 (0.45), residues: 66
  sheet: -3.01 (0.24), residues: 383
  loop : -3.99 (0.16), residues: 921

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 505 
 TYR   0.016   0.002   TYR B2021 
 PHE   0.015   0.002   PHE B1872 
 TRP   0.017   0.002   TRP B1563 
 HIS   0.006   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (11436)
  covalent geometry    : angle       0.79348 (15490)
  SS BOND              : bond        0.00632 (    6)
  SS BOND              : angle       1.92226 (   12)
  hydrogen bonds       : bond        0.04848 (  150)
  hydrogen bonds       : angle       8.64072 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 119
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.5629 (p90)
REVERT: B  227 TRP cc_start: 0.8308 (m100) cc_final: 0.7997 (m100)
REVERT: B  270 MET cc_start: 0.7750 (ppp) cc_final: 0.7516 (ppp)
REVERT: B  343 MET cc_start: 0.0130 (tpt) cc_final: -0.0954 (tpt)
REVERT: B  491 LEU cc_start: 0.7979 (mt) cc_final: 0.7350 (mt)
REVERT: B  613 LEU cc_start: 0.8813 (tp) cc_final: 0.8419 (tt)
REVERT: B 1700 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.7569 (m-90)
REVERT: B 1716 LEU cc_start: 0.9097 (mt) cc_final: 0.8632 (mp)
REVERT: B 1849 SER cc_start: 0.8768 (p) cc_final: 0.8540 (p)
REVERT: B 1868 MET cc_start: 0.4664 (mtt) cc_final: 0.4139 (mtt)
REVERT: B 1881 MET cc_start: 0.8658 (ppp) cc_final: 0.8053 (ppp)
REVERT: B 2015 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8661 (mp)
REVERT: B 2120 MET cc_start: 0.6705 (ptp) cc_final: 0.6366 (pmm)
  outliers start: 39
  outliers final: 18
  residues processed: 149
  average time/residue: 0.1084
  time to fit residues: 23.0428
Evaluate side-chains
  122 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  224 HIS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  505 ARG
Chi-restraints excluded: chain B residue  519 VAL
Chi-restraints excluded: chain B residue 1654 GLU
Chi-restraints excluded: chain B residue 1700 TRP
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1814 VAL
Chi-restraints excluded: chain B residue 1843 THR
Chi-restraints excluded: chain B residue 1876 ASP
Chi-restraints excluded: chain B residue 1901 LEU
Chi-restraints excluded: chain B residue 2015 ILE
Chi-restraints excluded: chain B residue 2095 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 103 optimal weight:    4.9990
   chunk 104 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS
B 244 ASN
** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 556 ASN
** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1986 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.077555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.060777 restraints weight = 63488.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.062139 restraints weight = 45695.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.063025 restraints weight = 36379.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.063426 restraints weight = 31298.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.064083 restraints weight = 28727.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11442  Z= 0.204
  Angle     :  0.739  10.461  15502  Z= 0.381
  Chirality :  0.047   0.194   1627
  Planarity :  0.005   0.094   1999
  Dihedral  :  6.248  28.420   1508
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.82 %
    Favored  : 85.18 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.84 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -4.85 (0.19), residues: 1370
  helix: -3.15 (0.51), residues: 66
  sheet: -2.70 (0.24), residues: 382
  loop : -3.70 (0.17), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  90 
 TYR   0.016   0.002   TYR B 209 
 PHE   0.020   0.002   PHE B1748 
 TRP   0.017   0.002   TRP B1563 
 HIS   0.006   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (11436)
  covalent geometry    : angle       0.73857 (15490)
  SS BOND              : bond        0.00457 (    6)
  SS BOND              : angle       1.32716 (   12)
  hydrogen bonds       : bond        0.04207 (  150)
  hydrogen bonds       : angle       7.97815 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 0.456 
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  270 MET cc_start: 0.7560 (ppp) cc_final: 0.6845 (ppp)
REVERT: B  289 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8875 (mm-40)
REVERT: B  343 MET cc_start: -0.0241 (tpt) cc_final: -0.1549 (tpt)
REVERT: B  357 ASN cc_start: 0.7034 (OUTLIER) cc_final: 0.6764 (p0)
REVERT: B  491 LEU cc_start: 0.7910 (mt) cc_final: 0.7200 (mt)
REVERT: B  523 PHE cc_start: 0.8999 (m-80) cc_final: 0.8794 (m-80)
REVERT: B  590 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8152 (pm20)
REVERT: B  613 LEU cc_start: 0.8777 (tp) cc_final: 0.8338 (tt)
REVERT: B  618 MET cc_start: 0.7779 (mtt) cc_final: 0.7560 (mtt)
REVERT: B 1700 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.7366 (m-90)
REVERT: B 1738 MET cc_start: 0.8444 (ttm) cc_final: 0.8196 (ttt)
REVERT: B 1793 TYR cc_start: 0.7923 (m-80) cc_final: 0.7671 (m-80)
REVERT: B 1868 MET cc_start: 0.4352 (mtt) cc_final: 0.3949 (mtt)
  outliers start: 39
  outliers final: 24
  residues processed: 136
  average time/residue: 0.0984
  time to fit residues: 19.5848
Evaluate side-chains
  117 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  224 HIS
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  289 GLN
Chi-restraints excluded: chain B residue  357 ASN
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  590 GLN
Chi-restraints excluded: chain B residue 1654 GLU
Chi-restraints excluded: chain B residue 1657 THR
Chi-restraints excluded: chain B residue 1700 TRP
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1814 VAL
Chi-restraints excluded: chain B residue 1901 LEU
Chi-restraints excluded: chain B residue 1956 TYR
Chi-restraints excluded: chain B residue 1988 MET
Chi-restraints excluded: chain B residue 2015 ILE
Chi-restraints excluded: chain B residue 2095 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 66 optimal weight:    0.3980
   chunk 15 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 126 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9980
   chunk 130 optimal weight:    0.8980
   chunk 71 optimal weight:    9.9990
   chunk 60 optimal weight:    0.8980
   chunk 122 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 379 HIS
B 556 ASN
B 597 HIS
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1570 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.079131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.061111 restraints weight = 63481.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.062640 restraints weight = 45468.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.063257 restraints weight = 36027.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.064282 restraints weight = 31739.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.064599 restraints weight = 28096.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11442  Z= 0.113
  Angle     :  0.674  10.604  15502  Z= 0.337
  Chirality :  0.046   0.183   1627
  Planarity :  0.005   0.090   1999
  Dihedral  :  5.613  26.192   1508
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.06 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -4.44 (0.20), residues: 1370
  helix: -3.39 (0.51), residues: 61
  sheet: -2.43 (0.25), residues: 390
  loop : -3.36 (0.18), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 475 
 TYR   0.010   0.001   TYR B 477 
 PHE   0.012   0.001   PHE B1979 
 TRP   0.012   0.001   TRP B1700 
 HIS   0.003   0.000   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (11436)
  covalent geometry    : angle       0.67360 (15490)
  SS BOND              : bond        0.00236 (    6)
  SS BOND              : angle       1.29415 (   12)
  hydrogen bonds       : bond        0.03307 (  150)
  hydrogen bonds       : angle       7.16241 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  292 MET cc_start: 0.8002 (ppp) cc_final: 0.7752 (ppp)
REVERT: B  343 MET cc_start: -0.0378 (tpt) cc_final: -0.1652 (tpt)
REVERT: B  357 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6835 (p0)
REVERT: B  420 HIS cc_start: 0.6511 (OUTLIER) cc_final: 0.6183 (m170)
REVERT: B  491 LEU cc_start: 0.7629 (mt) cc_final: 0.6997 (mt)
REVERT: B  523 PHE cc_start: 0.8989 (m-80) cc_final: 0.8712 (m-80)
REVERT: B  590 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8191 (pm20)
REVERT: B  613 LEU cc_start: 0.8627 (tp) cc_final: 0.8271 (tt)
REVERT: B  616 PHE cc_start: 0.8573 (m-80) cc_final: 0.8355 (m-80)
REVERT: B 1703 TYR cc_start: 0.6021 (p90) cc_final: 0.5814 (p90)
REVERT: B 1716 LEU cc_start: 0.9080 (mt) cc_final: 0.8599 (mp)
REVERT: B 1868 MET cc_start: 0.4356 (mtt) cc_final: 0.4020 (mtt)
REVERT: B 1883 MET cc_start: 0.8775 (mmm) cc_final: 0.8563 (mpp)
REVERT: B 2015 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8544 (mp)
REVERT: B 2034 GLU cc_start: 0.7817 (tp30) cc_final: 0.7606 (tp30)
  outliers start: 35
  outliers final: 13
  residues processed: 141
  average time/residue: 0.0934
  time to fit residues: 19.5351
Evaluate side-chains
  110 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  224 HIS
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  357 ASN
Chi-restraints excluded: chain B residue  363 TYR
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  590 GLN
Chi-restraints excluded: chain B residue 1654 GLU
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1849 SER
Chi-restraints excluded: chain B residue 1901 LEU
Chi-restraints excluded: chain B residue 1956 TYR
Chi-restraints excluded: chain B residue 2015 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 96 optimal weight:    0.0980
   chunk 60 optimal weight:    0.1980
   chunk 85 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9990
   chunk 128 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2046 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.077345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.059595 restraints weight = 64749.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.060934 restraints weight = 47038.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.061879 restraints weight = 38034.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.062554 restraints weight = 32745.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.062800 restraints weight = 29558.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11442  Z= 0.162
  Angle     :  0.698  11.776  15502  Z= 0.352
  Chirality :  0.046   0.182   1627
  Planarity :  0.005   0.093   1999
  Dihedral  :  5.619  24.809   1508
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.43 %
    Favored  : 86.57 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.29 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -4.30 (0.20), residues: 1370
  helix: -3.14 (0.50), residues: 73
  sheet: -2.31 (0.26), residues: 381
  loop : -3.29 (0.18), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  90 
 TYR   0.011   0.001   TYR B 144 
 PHE   0.010   0.001   PHE B1748 
 TRP   0.015   0.001   TRP B1563 
 HIS   0.005   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (11436)
  covalent geometry    : angle       0.69712 (15490)
  SS BOND              : bond        0.00495 (    6)
  SS BOND              : angle       1.56992 (   12)
  hydrogen bonds       : bond        0.03586 (  150)
  hydrogen bonds       : angle       7.09114 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  270 MET cc_start: 0.8600 (ppp) cc_final: 0.6931 (ppp)
REVERT: B  292 MET cc_start: 0.8017 (ppp) cc_final: 0.7786 (ppp)
REVERT: B  343 MET cc_start: -0.0237 (tpt) cc_final: -0.1504 (tpt)
REVERT: B  357 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6876 (p0)
REVERT: B  381 VAL cc_start: -0.0934 (OUTLIER) cc_final: -0.1425 (m)
REVERT: B  491 LEU cc_start: 0.7843 (mt) cc_final: 0.7186 (mt)
REVERT: B  523 PHE cc_start: 0.8987 (m-80) cc_final: 0.8683 (m-80)
REVERT: B  590 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8152 (pm20)
REVERT: B  613 LEU cc_start: 0.8672 (tp) cc_final: 0.8289 (tt)
REVERT: B 1700 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.7319 (m-90)
REVERT: B 1703 TYR cc_start: 0.6116 (p90) cc_final: 0.5873 (p90)
REVERT: B 1716 LEU cc_start: 0.9121 (mt) cc_final: 0.8837 (mp)
REVERT: B 1868 MET cc_start: 0.4540 (mtt) cc_final: 0.4215 (mtt)
REVERT: B 1901 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5832 (mp)
REVERT: B 2034 GLU cc_start: 0.8034 (tp30) cc_final: 0.7763 (tp30)
  outliers start: 36
  outliers final: 21
  residues processed: 130
  average time/residue: 0.0962
  time to fit residues: 18.8726
Evaluate side-chains
  119 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  224 HIS
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  357 ASN
Chi-restraints excluded: chain B residue  363 TYR
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  590 GLN
Chi-restraints excluded: chain B residue  596 ILE
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain B residue 1657 THR
Chi-restraints excluded: chain B residue 1700 TRP
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1901 LEU
Chi-restraints excluded: chain B residue 1956 TYR
Chi-restraints excluded: chain B residue 2015 ILE
Chi-restraints excluded: chain B residue 2095 LEU
Chi-restraints excluded: chain B residue 2193 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 81 optimal weight:    8.9990
   chunk 117 optimal weight:    0.0870
   chunk 94 optimal weight:    0.9980
   chunk 133 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 132 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    4.0164

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN
** B  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 556 ASN
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 699 GLN
** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1863 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.073272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.056916 restraints weight = 65525.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.058169 restraints weight = 47815.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.058700 restraints weight = 38631.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.059498 restraints weight = 34283.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.059808 restraints weight = 30786.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.5158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  11442  Z= 0.281
  Angle     :  0.811  13.281  15502  Z= 0.418
  Chirality :  0.048   0.192   1627
  Planarity :  0.006   0.103   1999
  Dihedral  :  6.302  25.555   1508
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 23.15
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.33 %
    Favored  : 84.60 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 22.94 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -4.42 (0.20), residues: 1370
  helix: -3.37 (0.45), residues: 66
  sheet: -2.36 (0.26), residues: 380
  loop : -3.38 (0.18), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  90 
 TYR   0.020   0.002   TYR B2021 
 PHE   0.015   0.002   PHE B2004 
 TRP   0.022   0.002   TRP B1563 
 HIS   0.008   0.002   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (11436)
  covalent geometry    : angle       0.80975 (15490)
  SS BOND              : bond        0.00492 (    6)
  SS BOND              : angle       1.54557 (   12)
  hydrogen bonds       : bond        0.04497 (  150)
  hydrogen bonds       : angle       7.80396 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 88
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  163 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9104 (pp)
REVERT: B  270 MET cc_start: 0.8778 (ppp) cc_final: 0.7104 (ppp)
REVERT: B  343 MET cc_start: 0.0155 (tpt) cc_final: -0.1104 (tpt)
REVERT: B  381 VAL cc_start: 0.0013 (OUTLIER) cc_final: -0.0206 (m)
REVERT: B  523 PHE cc_start: 0.8922 (m-80) cc_final: 0.8721 (m-80)
REVERT: B  558 MET cc_start: 0.7872 (mpp) cc_final: 0.7492 (mpp)
REVERT: B  590 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8184 (pm20)
REVERT: B  613 LEU cc_start: 0.8789 (tp) cc_final: 0.8355 (tt)
REVERT: B 1700 TRP cc_start: 0.8111 (OUTLIER) cc_final: 0.7340 (m-90)
REVERT: B 1746 MET cc_start: 0.7512 (tmm) cc_final: 0.7310 (tmm)
REVERT: B 1761 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8123 (mmp80)
REVERT: B 1868 MET cc_start: 0.4284 (mtt) cc_final: 0.3910 (mtt)
REVERT: B 1956 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7338 (p90)
  outliers start: 51
  outliers final: 34
  residues processed: 133
  average time/residue: 0.0911
  time to fit residues: 18.1285
Evaluate side-chains
  124 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 85
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  224 HIS
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  252 HIS
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  363 TYR
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  394 ILE
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  561 ILE
Chi-restraints excluded: chain B residue  590 GLN
Chi-restraints excluded: chain B residue  596 ILE
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain B residue  623 VAL
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain B residue 1654 GLU
Chi-restraints excluded: chain B residue 1657 THR
Chi-restraints excluded: chain B residue 1700 TRP
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1814 VAL
Chi-restraints excluded: chain B residue 1849 SER
Chi-restraints excluded: chain B residue 1901 LEU
Chi-restraints excluded: chain B residue 1920 TRP
Chi-restraints excluded: chain B residue 1956 TYR
Chi-restraints excluded: chain B residue 2015 ILE
Chi-restraints excluded: chain B residue 2095 LEU
Chi-restraints excluded: chain B residue 2171 ARG
Chi-restraints excluded: chain B residue 2193 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 125 optimal weight:    0.0570
   chunk 87 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 70 optimal weight:   20.0000
   chunk 121 optimal weight:    9.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 HIS
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 556 ASN
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2162 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.077422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.059634 restraints weight = 64484.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.061065 restraints weight = 46355.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.062060 restraints weight = 37064.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.062773 restraints weight = 31809.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.063118 restraints weight = 28594.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11442  Z= 0.114
  Angle     :  0.691  10.742  15502  Z= 0.345
  Chirality :  0.047   0.183   1627
  Planarity :  0.005   0.090   1999
  Dihedral  :  5.539  26.194   1508
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.63 %
    Favored  : 87.37 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 24.41 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -4.10 (0.21), residues: 1370
  helix: -3.05 (0.51), residues: 73
  sheet: -2.14 (0.27), residues: 377
  loop : -3.15 (0.18), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  90 
 TYR   0.011   0.001   TYR B 477 
 PHE   0.009   0.001   PHE B1990 
 TRP   0.013   0.001   TRP B 457 
 HIS   0.003   0.000   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (11436)
  covalent geometry    : angle       0.69025 (15490)
  SS BOND              : bond        0.00429 (    6)
  SS BOND              : angle       1.21757 (   12)
  hydrogen bonds       : bond        0.03188 (  150)
  hydrogen bonds       : angle       6.88658 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  214 MET cc_start: 0.8436 (tmm) cc_final: 0.8222 (tmm)
REVERT: B  270 MET cc_start: 0.8653 (ppp) cc_final: 0.7094 (ppp)
REVERT: B  343 MET cc_start: -0.0288 (tpt) cc_final: -0.1615 (tpt)
REVERT: B  357 ASN cc_start: 0.7067 (OUTLIER) cc_final: 0.6797 (p0)
REVERT: B  381 VAL cc_start: -0.0211 (OUTLIER) cc_final: -0.0413 (m)
REVERT: B  491 LEU cc_start: 0.7838 (mt) cc_final: 0.7263 (mt)
REVERT: B  523 PHE cc_start: 0.9048 (m-80) cc_final: 0.8735 (m-80)
REVERT: B  613 LEU cc_start: 0.8615 (tp) cc_final: 0.8399 (tp)
REVERT: B 1716 LEU cc_start: 0.9031 (mt) cc_final: 0.8740 (mp)
REVERT: B 1956 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7187 (p90)
  outliers start: 28
  outliers final: 16
  residues processed: 118
  average time/residue: 0.0871
  time to fit residues: 15.4757
Evaluate side-chains
  106 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  357 ASN
Chi-restraints excluded: chain B residue  363 TYR
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  596 ILE
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain B residue  623 VAL
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1956 TYR
Chi-restraints excluded: chain B residue 2015 ILE
Chi-restraints excluded: chain B residue 2193 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 122 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 99 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 71 optimal weight:   20.0000
   chunk 133 optimal weight:    9.9990
   chunk 96 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 556 ASN
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1781 ASN ** 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 = 0.3963 r_free = 0.3963 target = 0.071676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.055836 restraints weight = 64661.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.056984 restraints weight = 47106.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.057519 restraints weight = 38101.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.058269 restraints weight = 33783.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.058557 restraints weight = 30286.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.5721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.091  11442  Z= 0.338
  Angle     :  0.869  12.696  15502  Z= 0.448
  Chirality :  0.049   0.194   1627
  Planarity :  0.006   0.103   1999
  Dihedral  :  6.454  25.810   1508
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 27.12
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 16.28 %
    Favored  : 83.65 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 25.14 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -4.36 (0.20), residues: 1370
  helix: -3.40 (0.44), residues: 66
  sheet: -2.24 (0.27), residues: 350
  loop : -3.36 (0.17), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  90 
 TYR   0.025   0.003   TYR B2021 
 PHE   0.016   0.002   PHE B2004 
 TRP   0.022   0.002   TRP B1920 
 HIS   0.010   0.002   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 (11436)
  covalent geometry    : angle       0.86786 (15490)
  SS BOND              : bond        0.00552 (    6)
  SS BOND              : angle       1.60419 (   12)
  hydrogen bonds       : bond        0.04780 (  150)
  hydrogen bonds       : angle       7.96085 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 83
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  163 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9137 (pp)
REVERT: B  343 MET cc_start: 0.0350 (tpt) cc_final: -0.1134 (tpt)
REVERT: B  381 VAL cc_start: 0.0335 (OUTLIER) cc_final: 0.0119 (m)
REVERT: B  613 LEU cc_start: 0.8768 (tp) cc_final: 0.8504 (tp)
REVERT: B 1700 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.7234 (m-90)
REVERT: B 1956 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7403 (p90)
  outliers start: 36
  outliers final: 27
  residues processed: 114
  average time/residue: 0.0950
  time to fit residues: 16.2539
Evaluate side-chains
  108 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  363 TYR
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  561 ILE
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  596 ILE
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain B residue  623 VAL
Chi-restraints excluded: chain B residue 1654 GLU
Chi-restraints excluded: chain B residue 1657 THR
Chi-restraints excluded: chain B residue 1700 TRP
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1935 ILE
Chi-restraints excluded: chain B residue 1956 TYR
Chi-restraints excluded: chain B residue 2015 ILE
Chi-restraints excluded: chain B residue 2171 ARG
Chi-restraints excluded: chain B residue 2193 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 125 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 114 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 556 ASN
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1781 ASN ** 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 = 0.4019 r_free = 0.4019 target = 0.074593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.058472 restraints weight = 62492.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.059775 restraints weight = 45944.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.060518 restraints weight = 36647.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.061135 restraints weight = 31829.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.061546 restraints weight = 28811.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.5735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11442  Z= 0.162
  Angle     :  0.742  11.046  15502  Z= 0.374
  Chirality :  0.047   0.186   1627
  Planarity :  0.005   0.095   1999
  Dihedral  :  5.959  26.080   1508
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.36 %
    Favored  : 86.64 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 25.22 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -4.13 (0.21), residues: 1370
  helix: -3.28 (0.46), residues: 69
  sheet: -2.16 (0.27), residues: 361
  loop : -3.15 (0.18), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  90 
 TYR   0.025   0.002   TYR B2021 
 PHE   0.011   0.001   PHE B1979 
 TRP   0.016   0.002   TRP B 333 
 HIS   0.005   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (11436)
  covalent geometry    : angle       0.74160 (15490)
  SS BOND              : bond        0.00351 (    6)
  SS BOND              : angle       1.27612 (   12)
  hydrogen bonds       : bond        0.03648 (  150)
  hydrogen bonds       : angle       7.39062 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 87
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  163 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9114 (pp)
REVERT: B  203 MET cc_start: 0.7937 (ppp) cc_final: 0.7111 (ppp)
REVERT: B  270 MET cc_start: 0.8507 (ppp) cc_final: 0.6917 (ppp)
REVERT: B  343 MET cc_start: -0.0081 (tpt) cc_final: -0.2507 (tmm)
REVERT: B  381 VAL cc_start: 0.0479 (OUTLIER) cc_final: 0.0244 (m)
REVERT: B  410 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7533 (mtm)
REVERT: B  491 LEU cc_start: 0.8025 (mt) cc_final: 0.7474 (mt)
REVERT: B  523 PHE cc_start: 0.9115 (m-80) cc_final: 0.8859 (m-80)
REVERT: B  558 MET cc_start: 0.7799 (mpp) cc_final: 0.7478 (mpp)
REVERT: B  613 LEU cc_start: 0.8791 (tp) cc_final: 0.8542 (tp)
REVERT: B 1700 TRP cc_start: 0.7812 (OUTLIER) cc_final: 0.7082 (m-90)
REVERT: B 1716 LEU cc_start: 0.9219 (mt) cc_final: 0.8945 (mp)
REVERT: B 1844 LEU cc_start: 0.8353 (mt) cc_final: 0.8125 (mm)
REVERT: B 1881 MET cc_start: 0.8116 (ppp) cc_final: 0.7896 (ppp)
REVERT: B 1956 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7268 (p90)
  outliers start: 31
  outliers final: 24
  residues processed: 114
  average time/residue: 0.0865
  time to fit residues: 15.2209
Evaluate side-chains
  112 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 83
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  224 HIS
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  363 TYR
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  596 ILE
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain B residue  623 VAL
Chi-restraints excluded: chain B residue 1654 GLU
Chi-restraints excluded: chain B residue 1700 TRP
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1814 VAL
Chi-restraints excluded: chain B residue 1849 SER
Chi-restraints excluded: chain B residue 1956 TYR
Chi-restraints excluded: chain B residue 2015 ILE
Chi-restraints excluded: chain B residue 2171 ARG
Chi-restraints excluded: chain B residue 2193 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 135 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 105 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.074229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.057549 restraints weight = 65562.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.058938 restraints weight = 46102.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.059905 restraints weight = 36535.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.060569 restraints weight = 31167.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.060831 restraints weight = 27950.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.5829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11442  Z= 0.141
  Angle     :  0.722  10.514  15502  Z= 0.361
  Chirality :  0.046   0.184   1627
  Planarity :  0.005   0.093   1999
  Dihedral  :  5.700  25.381   1508
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.72 %
    Favored  : 86.28 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 25.22 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -4.01 (0.21), residues: 1370
  helix: -3.36 (0.43), residues: 73
  sheet: -1.93 (0.28), residues: 344
  loop : -3.11 (0.18), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B1687 
 TYR   0.011   0.001   TYR B 209 
 PHE   0.014   0.001   PHE B1748 
 TRP   0.017   0.001   TRP B 333 
 HIS   0.004   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11436)
  covalent geometry    : angle       0.72121 (15490)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       1.18810 (   12)
  hydrogen bonds       : bond        0.03482 (  150)
  hydrogen bonds       : angle       7.12196 (  384)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  163 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9169 (pp)
REVERT: B  203 MET cc_start: 0.7911 (ppp) cc_final: 0.7148 (ppp)
REVERT: B  270 MET cc_start: 0.8420 (ppp) cc_final: 0.6718 (ppp)
REVERT: B  343 MET cc_start: -0.0180 (tpt) cc_final: -0.2677 (tmm)
REVERT: B  491 LEU cc_start: 0.8110 (mt) cc_final: 0.7559 (mt)
REVERT: B  523 PHE cc_start: 0.9125 (m-80) cc_final: 0.8884 (m-80)
REVERT: B  558 MET cc_start: 0.7780 (mpp) cc_final: 0.7527 (mpp)
REVERT: B  613 LEU cc_start: 0.8717 (tp) cc_final: 0.8506 (tp)
REVERT: B 1691 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6134 (mp0)
REVERT: B 1700 TRP cc_start: 0.7784 (OUTLIER) cc_final: 0.7547 (m-10)
REVERT: B 1716 LEU cc_start: 0.9201 (mt) cc_final: 0.8956 (mp)
REVERT: B 1844 LEU cc_start: 0.8396 (mt) cc_final: 0.8166 (mm)
REVERT: B 1956 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7228 (p90)
  outliers start: 33
  outliers final: 25
  residues processed: 114
  average time/residue: 0.0841
  time to fit residues: 14.8455
Evaluate side-chains
  113 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  224 HIS
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  363 TYR
Chi-restraints excluded: chain B residue  474 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  596 ILE
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain B residue  623 VAL
Chi-restraints excluded: chain B residue 1654 GLU
Chi-restraints excluded: chain B residue 1691 GLU
Chi-restraints excluded: chain B residue 1700 TRP
Chi-restraints excluded: chain B residue 1787 LEU
Chi-restraints excluded: chain B residue 1814 VAL
Chi-restraints excluded: chain B residue 1849 SER
Chi-restraints excluded: chain B residue 1943 VAL
Chi-restraints excluded: chain B residue 1956 TYR
Chi-restraints excluded: chain B residue 2015 ILE
Chi-restraints excluded: chain B residue 2171 ARG
Chi-restraints excluded: chain B residue 2193 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 91 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 135 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.076098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.060167 restraints weight = 65018.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.061533 restraints weight = 45893.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.062473 restraints weight = 36338.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.063131 restraints weight = 30979.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.063466 restraints weight = 27713.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.5918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11442  Z= 0.132
  Angle     :  0.717  13.998  15502  Z= 0.356
  Chirality :  0.046   0.195   1627
  Planarity :  0.005   0.091   1999
  Dihedral  :  5.540  24.375   1508
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.70 %
    Favored  : 87.30 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 25.47 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.52 %
    Cis-general     : 0.08 %
    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 are not related in a simple way.
  whole: -3.77 (0.21), residues: 1370
  helix: -2.95 (0.49), residues: 63
  sheet: -1.78 (0.28), residues: 344
  loop : -2.97 (0.18), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  90 
 TYR   0.015   0.001   TYR B 368 
 PHE   0.014   0.001   PHE B1979 
 TRP   0.017   0.001   TRP B 333 
 HIS   0.004   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (11436)
  covalent geometry    : angle       0.71630 (15490)
  SS BOND              : bond        0.00335 (    6)
  SS BOND              : angle       1.16572 (   12)
  hydrogen bonds       : bond        0.03315 (  150)
  hydrogen bonds       : angle       6.99349 (  384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2118.86 seconds
wall clock time: 37 minutes 26.52 seconds (2246.52 seconds total)