Starting phenix.real_space_refine
on Sun Dec 29 05:05:29 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xqj_33398/12_2024/7xqj_33398.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xqj_33398/12_2024/7xqj_33398.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xqj_33398/12_2024/7xqj_33398.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xqj_33398/12_2024/7xqj_33398.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xqj_33398/12_2024/7xqj_33398.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xqj_33398/12_2024/7xqj_33398.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      54      5.16       5
     C    6642      2.51       5
     N    1590      2.21       5
     O    1674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 9960
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1660
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 3.79, per 1000 atoms: 0.38
  Number of scatterers: 9960
  At special positions: 0
  Unit cell: (102.608, 104.304, 101.76, 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      54     16.00
     O    1674      8.00
     N    1590      7.00
     C    6642      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  61 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  65 " - pdb=" SG  CYS A 187 " 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: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2316

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 6 sheets defined
      73.0% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS A  13 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 33
      removed outlier: 3.738A  pdb=" N   ARG A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 40
      removed outlier: 3.544A  pdb=" N   GLY A  38 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 45
      removed outlier: 3.943A  pdb=" N   TRP A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 85
      removed outlier: 3.523A  pdb=" N   PHE A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 88
      No H-bonds generated for 'chain 'A' and resid 86 through 88'
    Processing helix  chain 'A' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU A  93 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 177
    Processing helix  chain 'A' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS B  13 " --> pdb=" O   LYS B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 33
      removed outlier: 3.739A  pdb=" N   ARG B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 40
      removed outlier: 3.544A  pdb=" N   GLY B  38 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 3.944A  pdb=" N   TRP B  45 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL B  64 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 85
      removed outlier: 3.522A  pdb=" N   PHE B  77 " --> pdb=" O   SER B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU B  93 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 177
    Processing helix  chain 'B' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS C  13 " --> pdb=" O   LYS C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 33
      removed outlier: 3.739A  pdb=" N   ARG C  33 " --> pdb=" O   LEU C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 40
      removed outlier: 3.545A  pdb=" N   GLY C  38 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA C  40 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 45
      removed outlier: 3.943A  pdb=" N   TRP C  45 " --> pdb=" O   VAL C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL C  64 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 85
      removed outlier: 3.522A  pdb=" N   PHE C  77 " --> pdb=" O   SER C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 88
      No H-bonds generated for 'chain 'C' and resid 86 through 88'
    Processing helix  chain 'C' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU C  93 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 177
    Processing helix  chain 'C' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS C 206 " --> pdb=" O   ARG C 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS D  13 " --> pdb=" O   LYS D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 33
      removed outlier: 3.738A  pdb=" N   ARG D  33 " --> pdb=" O   LEU D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 33 through 40
      removed outlier: 3.544A  pdb=" N   GLY D  38 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA D  40 " --> pdb=" O   LEU D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 45
      removed outlier: 3.944A  pdb=" N   TRP D  45 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL D  64 " --> pdb=" O   GLY D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 85
      removed outlier: 3.523A  pdb=" N   PHE D  77 " --> pdb=" O   SER D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 88
      No H-bonds generated for 'chain 'D' and resid 86 through 88'
    Processing helix  chain 'D' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU D  93 " --> pdb=" O   THR D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 177
    Processing helix  chain 'D' and resid 202 through 238
      removed outlier: 3.718A  pdb=" N   LYS D 206 " --> pdb=" O   ARG D 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS E  13 " --> pdb=" O   LYS E   9 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 19 through 33
      removed outlier: 3.738A  pdb=" N   ARG E  33 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 33 through 40
      removed outlier: 3.544A  pdb=" N   GLY E  38 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA E  40 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 45
      removed outlier: 3.943A  pdb=" N   TRP E  45 " --> pdb=" O   VAL E  41 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL E  64 " --> pdb=" O   GLY E  60 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 85
      removed outlier: 3.522A  pdb=" N   PHE E  77 " --> pdb=" O   SER E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 88
      No H-bonds generated for 'chain 'E' and resid 86 through 88'
    Processing helix  chain 'E' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU E  93 " --> pdb=" O   THR E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 150 through 177
    Processing helix  chain 'E' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS E 206 " --> pdb=" O   ARG E 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 7 through 15
      removed outlier: 4.903A  pdb=" N   LYS F  13 " --> pdb=" O   LYS F   9 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 19 through 33
      removed outlier: 3.739A  pdb=" N   ARG F  33 " --> pdb=" O   LEU F  29 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 33 through 40
      removed outlier: 3.545A  pdb=" N   GLY F  38 " --> pdb=" O   ILE F  34 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA F  40 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 45
      removed outlier: 3.944A  pdb=" N   TRP F  45 " --> pdb=" O   VAL F  41 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 60 through 70
      removed outlier: 3.874A  pdb=" N   VAL F  64 " --> pdb=" O   GLY F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 85
      removed outlier: 3.522A  pdb=" N   PHE F  77 " --> pdb=" O   SER F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 88
      No H-bonds generated for 'chain 'F' and resid 86 through 88'
    Processing helix  chain 'F' and resid 89 through 107
      removed outlier: 3.714A  pdb=" N   LEU F  93 " --> pdb=" O   THR F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 150 through 177
    Processing helix  chain 'F' and resid 202 through 238
      removed outlier: 3.717A  pdb=" N   LYS F 206 " --> pdb=" O   ARG F 202 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG A  53 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG B  53 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG C  53 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG D  53 " --> pdb=" O   PHE D 199 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54
      removed outlier: 3.503A  pdb=" N   ARG E  53 " --> pdb=" O   PHE E 199 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54
      removed outlier: 3.502A  pdb=" N   ARG F  53 " --> pdb=" O   PHE F 199 " (cutoff:3.500A)

    636 hydrogen bonds defined for protein.
    1890 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: 2.62

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2934
        1.34 -     1.46: 2224
        1.46 -     1.57: 4988
        1.57 -     1.69: 0
        1.69 -     1.80: 72
  Bond restraints: 10218
  Sorted by residual:
  bond pdb=" C   VAL C  87 "
       pdb=" N   PRO C  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.31e+00
  bond pdb=" C   VAL D  87 "
       pdb=" N   PRO D  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.21e+00
  bond pdb=" C   VAL A  87 "
       pdb=" N   PRO A  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.15e+00
  bond pdb=" C   VAL F  87 "
       pdb=" N   PRO F  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.09e+00
  bond pdb=" C   VAL E  87 "
       pdb=" N   PRO E  88 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.09e+00
  ... (remaining 10213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 13172
        1.65 -     3.30: 508
        3.30 -     4.95: 108
        4.95 -     6.61: 24
        6.61 -     8.26: 12
  Bond angle restraints: 13824
  Sorted by residual:
  angle pdb=" N   GLU B  42 "
        pdb=" CA  GLU B  42 "
        pdb=" C   GLU B  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.89    5.01 1.31e+00 5.83e-01 1.46e+01
  angle pdb=" N   GLU A  42 "
        pdb=" CA  GLU A  42 "
        pdb=" C   GLU A  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.90    5.00 1.31e+00 5.83e-01 1.46e+01
  angle pdb=" N   GLU D  42 "
        pdb=" CA  GLU D  42 "
        pdb=" C   GLU D  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.91    4.99 1.31e+00 5.83e-01 1.45e+01
  angle pdb=" N   GLU C  42 "
        pdb=" CA  GLU C  42 "
        pdb=" C   GLU C  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.93    4.97 1.31e+00 5.83e-01 1.44e+01
  angle pdb=" N   GLU F  42 "
        pdb=" CA  GLU F  42 "
        pdb=" C   GLU F  42 "
      ideal   model   delta    sigma   weight residual
     112.90  107.93    4.97 1.31e+00 5.83e-01 1.44e+01
  ... (remaining 13819 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.83: 5124
       13.83 -    27.65: 469
       27.65 -    41.48: 200
       41.48 -    55.30: 120
       55.30 -    69.13: 54
  Dihedral angle restraints: 5967
    sinusoidal: 2385
      harmonic: 3582
  Sorted by residual:
  dihedral pdb=" CA  PRO B 193 "
           pdb=" C   PRO B 193 "
           pdb=" N   HIS B 194 "
           pdb=" CA  HIS B 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.31  -19.69     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  PRO F 193 "
           pdb=" C   PRO F 193 "
           pdb=" N   HIS F 194 "
           pdb=" CA  HIS F 194 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.33  -19.67     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  PRO A 193 "
           pdb=" C   PRO A 193 "
           pdb=" N   HIS A 194 "
           pdb=" CA  HIS A 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.35  -19.65     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 5964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 998
       0.035 -    0.071: 373
       0.071 -    0.106: 157
       0.106 -    0.141: 32
       0.141 -    0.177: 12
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" CA  ALA E   6 "
            pdb=" N   ALA E   6 "
            pdb=" C   ALA E   6 "
            pdb=" CB  ALA E   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.66   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  ALA C   6 "
            pdb=" N   ALA C   6 "
            pdb=" C   ALA C   6 "
            pdb=" CB  ALA C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.66   -0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CA  ALA F   6 "
            pdb=" N   ALA F   6 "
            pdb=" C   ALA F   6 "
            pdb=" CB  ALA F   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.66   -0.17 2.00e-01 2.50e+01 7.60e-01
  ... (remaining 1569 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  87 "    0.035 5.00e-02 4.00e+02   5.19e-02 4.30e+00
        pdb=" N   PRO A  88 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F  87 "    0.035 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO F  88 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO F  88 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO F  88 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E  87 "    0.035 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO E  88 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO E  88 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  88 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 110
        2.60 -     3.18: 8257
        3.18 -     3.75: 15835
        3.75 -     4.33: 18548
        4.33 -     4.90: 30865
  Nonbonded interactions: 73615
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C  54 "
            pdb=" SG  CYS C 198 "
     model   vdw
     2.026 3.760
  nonbonded pdb=" SG  CYS E  54 "
            pdb=" SG  CYS E 198 "
     model   vdw
     2.026 3.760
  nonbonded pdb=" SG  CYS D  54 "
            pdb=" SG  CYS D 198 "
     model   vdw
     2.027 3.760
  nonbonded pdb=" SG  CYS B  54 "
            pdb=" SG  CYS B 198 "
     model   vdw
     2.027 3.760
  nonbonded pdb=" SG  CYS F  54 "
            pdb=" SG  CYS F 198 "
     model   vdw
     2.027 3.760
  ... (remaining 73610 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.830
  Find NCS groups from input model:        0.300
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  10218  Z= 0.418
  Angle     :  0.838   8.257  13824  Z= 0.488
  Chirality :  0.045   0.177   1572
  Planarity :  0.007   0.052   1662
  Dihedral  : 15.982  69.127   3642
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 11.48 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.20), residues: 1200
  helix: -1.68 (0.14), residues: 822
  sheet:  2.82 (0.55), residues: 60
  loop : -2.92 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  25 
 HIS   0.003   0.001   HIS E  74 
 PHE   0.011   0.002   PHE C  97 
 TYR   0.008   0.001   TYR D  92 
 ARG   0.004   0.001   ARG F 148 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 259
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7359 (p90)
REVERT: A   47 ASP cc_start: 0.8821 (p0) cc_final: 0.8566 (p0)
REVERT: A  100 MET cc_start: 0.9574 (ttp) cc_final: 0.8899 (tmm)
REVERT: A  101 ARG cc_start: 0.9461 (ttm170) cc_final: 0.9100 (ttp-110)
REVERT: A  213 MET cc_start: 0.9231 (mmm) cc_final: 0.8886 (mmp)
REVERT: A  224 ASN cc_start: 0.8962 (m110) cc_final: 0.8571 (m110)
REVERT: A  227 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9124 (tm-30)
REVERT: B   17 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7252 (p90)
REVERT: B  100 MET cc_start: 0.9586 (ttp) cc_final: 0.9010 (ppp)
REVERT: B  101 ARG cc_start: 0.9385 (ttm170) cc_final: 0.9025 (ttp-110)
REVERT: B  104 GLU cc_start: 0.9417 (tp30) cc_final: 0.9077 (mm-30)
REVERT: B  224 ASN cc_start: 0.8974 (m110) cc_final: 0.8561 (m110)
REVERT: B  227 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9010 (tm-30)
REVERT: C   17 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7324 (p90)
REVERT: C  100 MET cc_start: 0.9549 (ttp) cc_final: 0.9031 (ppp)
REVERT: C  101 ARG cc_start: 0.9407 (ttm170) cc_final: 0.9029 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9242 (tm-30)
REVERT: D   17 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7089 (p90)
REVERT: D   47 ASP cc_start: 0.8790 (p0) cc_final: 0.8497 (p0)
REVERT: D   81 GLN cc_start: 0.9439 (tt0) cc_final: 0.9198 (tt0)
REVERT: D  100 MET cc_start: 0.9557 (ttp) cc_final: 0.9050 (tmm)
REVERT: D  101 ARG cc_start: 0.9439 (ttm170) cc_final: 0.9220 (ttp-110)
REVERT: D  104 GLU cc_start: 0.9472 (tp30) cc_final: 0.9245 (mm-30)
REVERT: D  213 MET cc_start: 0.9251 (mmm) cc_final: 0.8935 (mmp)
REVERT: D  224 ASN cc_start: 0.9021 (m110) cc_final: 0.8658 (m110)
REVERT: D  227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9191 (tm-30)
REVERT: E   17 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7235 (p90)
REVERT: E  100 MET cc_start: 0.9585 (ttp) cc_final: 0.9013 (ppp)
REVERT: E  101 ARG cc_start: 0.9386 (ttm170) cc_final: 0.9019 (ttp-110)
REVERT: E  104 GLU cc_start: 0.9413 (tp30) cc_final: 0.9076 (mm-30)
REVERT: E  224 ASN cc_start: 0.8972 (m110) cc_final: 0.8559 (m110)
REVERT: E  227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9021 (tm-30)
REVERT: F   17 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7395 (p90)
REVERT: F  100 MET cc_start: 0.9553 (ttp) cc_final: 0.9040 (ppp)
REVERT: F  101 ARG cc_start: 0.9408 (ttm170) cc_final: 0.9036 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9238 (tm-30)
  outliers start: 66
  outliers final: 13
  residues processed: 307
  average time/residue: 0.2132
  time to fit residues: 91.2452
Evaluate side-chains
  204 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  194 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A  74 HIS
A 224 ASN
B  74 HIS
B  81 GLN
B 224 ASN
C  74 HIS
D  15 GLN
D  74 HIS
D 224 ASN
E  74 HIS
E  81 GLN
E 224 ASN
F  74 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10218  Z= 0.270
  Angle     :  0.704   8.071  13824  Z= 0.367
  Chirality :  0.039   0.156   1572
  Planarity :  0.004   0.036   1662
  Dihedral  :  7.530  54.300   1352
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 19.95 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.25), residues: 1200
  helix:  0.43 (0.18), residues: 846
  sheet:  3.08 (0.59), residues: 60
  loop : -2.81 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  25 
 HIS   0.003   0.001   HIS C 194 
 PHE   0.013   0.001   PHE C  30 
 TYR   0.009   0.001   TYR A  92 
 ARG   0.004   0.001   ARG F  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 190
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7572 (p90)
REVERT: A   47 ASP cc_start: 0.8847 (p0) cc_final: 0.8627 (p0)
REVERT: A  100 MET cc_start: 0.9409 (ttp) cc_final: 0.9119 (ppp)
REVERT: A  101 ARG cc_start: 0.9462 (ttm170) cc_final: 0.9092 (ttp80)
REVERT: A  213 MET cc_start: 0.9208 (mmm) cc_final: 0.8897 (mmp)
REVERT: A  224 ASN cc_start: 0.8853 (m-40) cc_final: 0.8496 (m110)
REVERT: A  227 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9159 (tm-30)
REVERT: B   17 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7470 (p90)
REVERT: B  100 MET cc_start: 0.9410 (ttp) cc_final: 0.9134 (ppp)
REVERT: B  101 ARG cc_start: 0.9389 (ttm170) cc_final: 0.9143 (ttp80)
REVERT: B  224 ASN cc_start: 0.8929 (m-40) cc_final: 0.8491 (m110)
REVERT: B  227 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9053 (tm-30)
REVERT: C   17 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7423 (p90)
REVERT: C  100 MET cc_start: 0.9380 (ttp) cc_final: 0.9049 (ppp)
REVERT: C  101 ARG cc_start: 0.9412 (ttm170) cc_final: 0.9132 (ttp80)
REVERT: C  227 GLU cc_start: 0.9435 (tm-30) cc_final: 0.9221 (tm-30)
REVERT: D   17 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7343 (p90)
REVERT: D   47 ASP cc_start: 0.8828 (p0) cc_final: 0.8602 (p0)
REVERT: D  100 MET cc_start: 0.9423 (ttp) cc_final: 0.9174 (ppp)
REVERT: D  101 ARG cc_start: 0.9440 (ttm170) cc_final: 0.9163 (ttp80)
REVERT: D  213 MET cc_start: 0.9226 (mmm) cc_final: 0.8961 (mmp)
REVERT: D  224 ASN cc_start: 0.8902 (m-40) cc_final: 0.8555 (m110)
REVERT: D  227 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9199 (tm-30)
REVERT: E   17 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7479 (p90)
REVERT: E  100 MET cc_start: 0.9409 (ttp) cc_final: 0.9132 (ppp)
REVERT: E  101 ARG cc_start: 0.9391 (ttm170) cc_final: 0.9138 (ttp80)
REVERT: E  224 ASN cc_start: 0.8919 (m-40) cc_final: 0.8491 (m110)
REVERT: E  227 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9048 (tm-30)
REVERT: F   17 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7448 (p90)
REVERT: F  100 MET cc_start: 0.9374 (ttp) cc_final: 0.9049 (ppp)
REVERT: F  101 ARG cc_start: 0.9410 (ttm170) cc_final: 0.9130 (ttp80)
REVERT: F  227 GLU cc_start: 0.9435 (tm-30) cc_final: 0.9220 (tm-30)
  outliers start: 71
  outliers final: 37
  residues processed: 245
  average time/residue: 0.1817
  time to fit residues: 65.4393
Evaluate side-chains
  212 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 169
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   65 CYS
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  194 HIS
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  194 HIS
Chi-restraints excluded: chain F residue  228 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 33 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 108 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN
E  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10218  Z= 0.171
  Angle     :  0.666   8.167  13824  Z= 0.339
  Chirality :  0.039   0.168   1572
  Planarity :  0.004   0.032   1662
  Dihedral  :  7.314  54.429   1352
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 21.22 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1200
  helix:  1.00 (0.18), residues: 852
  sheet:  3.38 (0.61), residues: 60
  loop : -2.64 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP C  25 
 HIS   0.002   0.001   HIS D 194 
 PHE   0.015   0.001   PHE B  30 
 TYR   0.015   0.001   TYR D  92 
 ARG   0.004   0.000   ARG B  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 203
  time to evaluate  : 1.124 
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: A   17 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7393 (p90)
REVERT: A   47 ASP cc_start: 0.8787 (p0) cc_final: 0.8578 (p0)
REVERT: A   48 GLU cc_start: 0.9201 (tp30) cc_final: 0.8665 (tm-30)
REVERT: A   81 GLN cc_start: 0.9465 (tt0) cc_final: 0.9257 (tt0)
REVERT: A  100 MET cc_start: 0.9410 (ttp) cc_final: 0.9145 (ppp)
REVERT: A  101 ARG cc_start: 0.9457 (ttm170) cc_final: 0.9084 (ttp-110)
REVERT: A  213 MET cc_start: 0.9157 (mmm) cc_final: 0.8830 (mmp)
REVERT: A  224 ASN cc_start: 0.8802 (m-40) cc_final: 0.8436 (m110)
REVERT: A  227 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9111 (tm-30)
REVERT: B   17 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7428 (p90)
REVERT: B   48 GLU cc_start: 0.9186 (tp30) cc_final: 0.8513 (tm-30)
REVERT: B   49 GLN cc_start: 0.8842 (tt0) cc_final: 0.8454 (tp40)
REVERT: B  101 ARG cc_start: 0.9383 (ttm170) cc_final: 0.8948 (ttp-110)
REVERT: B  224 ASN cc_start: 0.8865 (m-40) cc_final: 0.8452 (m110)
REVERT: B  227 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9010 (tm-30)
REVERT: C   17 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7407 (p90)
REVERT: C  100 MET cc_start: 0.9315 (ttp) cc_final: 0.9062 (ppp)
REVERT: C  101 ARG cc_start: 0.9423 (ttm170) cc_final: 0.9043 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9203 (tm-30)
REVERT: D   17 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7109 (p90)
REVERT: D   48 GLU cc_start: 0.9162 (tp30) cc_final: 0.8445 (tm-30)
REVERT: D   49 GLN cc_start: 0.8749 (tt0) cc_final: 0.8444 (tp40)
REVERT: D  100 MET cc_start: 0.9406 (ttp) cc_final: 0.9177 (ppp)
REVERT: D  101 ARG cc_start: 0.9442 (ttm170) cc_final: 0.9175 (ttp-110)
REVERT: D  213 MET cc_start: 0.9194 (mmm) cc_final: 0.8909 (mmp)
REVERT: D  224 ASN cc_start: 0.8871 (m-40) cc_final: 0.8518 (m110)
REVERT: D  227 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9170 (tm-30)
REVERT: E   17 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7438 (p90)
REVERT: E   48 GLU cc_start: 0.9212 (tp30) cc_final: 0.8455 (tm-30)
REVERT: E   49 GLN cc_start: 0.8850 (tt0) cc_final: 0.8427 (tp40)
REVERT: E  101 ARG cc_start: 0.9384 (ttm170) cc_final: 0.8942 (ttp-110)
REVERT: E  224 ASN cc_start: 0.8885 (m-40) cc_final: 0.8465 (m110)
REVERT: E  227 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9009 (tm-30)
REVERT: F   17 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7414 (p90)
REVERT: F  100 MET cc_start: 0.9318 (ttp) cc_final: 0.9060 (ppp)
REVERT: F  101 ARG cc_start: 0.9421 (ttm170) cc_final: 0.9039 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9195 (tm-30)
  outliers start: 64
  outliers final: 36
  residues processed: 249
  average time/residue: 0.1976
  time to fit residues: 70.9577
Evaluate side-chains
  229 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 187
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  194 HIS
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  187 CYS
Chi-restraints excluded: chain C residue  194 HIS
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   61 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  194 HIS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  187 CYS
Chi-restraints excluded: chain F residue  194 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    0.2980
   chunk 82 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 115 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B  81 GLN
E  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10218  Z= 0.166
  Angle     :  0.657   7.782  13824  Z= 0.337
  Chirality :  0.039   0.177   1572
  Planarity :  0.004   0.030   1662
  Dihedral  :  6.979  55.764   1348
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 22.13 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.25), residues: 1200
  helix:  1.47 (0.19), residues: 822
  sheet:  2.85 (0.66), residues: 66
  loop : -2.12 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP C  25 
 HIS   0.002   0.001   HIS A  74 
 PHE   0.013   0.001   PHE B  30 
 TYR   0.015   0.001   TYR D  92 
 ARG   0.005   0.000   ARG F  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 198
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7199 (p90)
REVERT: A   42 GLU cc_start: 0.8336 (pp20) cc_final: 0.8050 (pp20)
REVERT: A   47 ASP cc_start: 0.8794 (p0) cc_final: 0.8584 (p0)
REVERT: A   48 GLU cc_start: 0.9167 (tp30) cc_final: 0.8481 (tm-30)
REVERT: A   49 GLN cc_start: 0.8822 (tt0) cc_final: 0.8505 (tp40)
REVERT: A  100 MET cc_start: 0.9398 (ttp) cc_final: 0.9144 (ppp)
REVERT: A  101 ARG cc_start: 0.9458 (ttm170) cc_final: 0.9089 (ttp-110)
REVERT: A  213 MET cc_start: 0.9124 (mmm) cc_final: 0.8812 (mmp)
REVERT: A  224 ASN cc_start: 0.8802 (m-40) cc_final: 0.8409 (m110)
REVERT: A  227 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9106 (tm-30)
REVERT: B   17 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7468 (p90)
REVERT: B  101 ARG cc_start: 0.9384 (ttm170) cc_final: 0.8954 (ttp-110)
REVERT: B  213 MET cc_start: 0.9162 (mmm) cc_final: 0.8951 (mmp)
REVERT: B  224 ASN cc_start: 0.8841 (m-40) cc_final: 0.8611 (m110)
REVERT: B  227 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9026 (tm-30)
REVERT: C   17 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7471 (p90)
REVERT: C   48 GLU cc_start: 0.9155 (tp30) cc_final: 0.8664 (tm-30)
REVERT: C  100 MET cc_start: 0.9329 (ttp) cc_final: 0.9080 (ppp)
REVERT: C  101 ARG cc_start: 0.9417 (ttm170) cc_final: 0.9039 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9405 (tm-30) cc_final: 0.9195 (tm-30)
REVERT: D   17 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.6828 (p90)
REVERT: D   48 GLU cc_start: 0.9071 (tp30) cc_final: 0.8416 (tm-30)
REVERT: D   49 GLN cc_start: 0.8749 (tt0) cc_final: 0.8416 (tp40)
REVERT: D  100 MET cc_start: 0.9409 (ttp) cc_final: 0.9198 (ppp)
REVERT: D  101 ARG cc_start: 0.9422 (ttm170) cc_final: 0.9155 (ttp-110)
REVERT: D  213 MET cc_start: 0.9198 (mmm) cc_final: 0.8925 (mmp)
REVERT: D  224 ASN cc_start: 0.8831 (m-40) cc_final: 0.8464 (m110)
REVERT: D  227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9174 (tm-30)
REVERT: E   17 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7476 (p90)
REVERT: E  101 ARG cc_start: 0.9387 (ttm170) cc_final: 0.8954 (ttp-110)
REVERT: E  213 MET cc_start: 0.9164 (mmm) cc_final: 0.8947 (mmp)
REVERT: E  224 ASN cc_start: 0.8842 (m-40) cc_final: 0.8615 (m110)
REVERT: E  227 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9026 (tm-30)
REVERT: F   17 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7466 (p90)
REVERT: F   48 GLU cc_start: 0.9176 (tp30) cc_final: 0.8619 (tm-30)
REVERT: F  100 MET cc_start: 0.9326 (ttp) cc_final: 0.9084 (ppp)
REVERT: F  101 ARG cc_start: 0.9414 (ttm170) cc_final: 0.9037 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9403 (tm-30) cc_final: 0.9193 (tm-30)
  outliers start: 57
  outliers final: 24
  residues processed: 235
  average time/residue: 0.2044
  time to fit residues: 68.9553
Evaluate side-chains
  215 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   61 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   67 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 80 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 59 optimal weight:    8.9990
   chunk 104 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10218  Z= 0.269
  Angle     :  0.676   7.596  13824  Z= 0.351
  Chirality :  0.040   0.176   1572
  Planarity :  0.004   0.032   1662
  Dihedral  :  6.245  53.411   1336
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.95 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.25), residues: 1200
  helix:  1.64 (0.19), residues: 822
  sheet:  2.79 (0.65), residues: 66
  loop : -1.94 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP E  25 
 HIS   0.003   0.001   HIS A 194 
 PHE   0.019   0.001   PHE E  30 
 TYR   0.020   0.001   TYR B  66 
 ARG   0.004   0.000   ARG C  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 185
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7485 (p90)
REVERT: A   48 GLU cc_start: 0.9202 (tp30) cc_final: 0.8679 (tm-30)
REVERT: A   72 ILE cc_start: 0.9590 (pt) cc_final: 0.9348 (tt)
REVERT: A  100 MET cc_start: 0.9392 (ttp) cc_final: 0.9139 (ppp)
REVERT: A  101 ARG cc_start: 0.9459 (ttm170) cc_final: 0.9086 (ttp-110)
REVERT: A  213 MET cc_start: 0.9151 (mmm) cc_final: 0.8859 (mmp)
REVERT: A  224 ASN cc_start: 0.8826 (m-40) cc_final: 0.8457 (m110)
REVERT: A  227 GLU cc_start: 0.9439 (tm-30) cc_final: 0.9149 (tm-30)
REVERT: B   17 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7659 (p90)
REVERT: B  101 ARG cc_start: 0.9404 (ttm170) cc_final: 0.9063 (ttp-110)
REVERT: B  213 MET cc_start: 0.9193 (mmm) cc_final: 0.8911 (mmp)
REVERT: B  224 ASN cc_start: 0.9091 (m-40) cc_final: 0.8660 (m110)
REVERT: B  227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9042 (tm-30)
REVERT: C   17 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7748 (p90)
REVERT: C  100 MET cc_start: 0.9343 (ttp) cc_final: 0.9091 (ppp)
REVERT: C  101 ARG cc_start: 0.9418 (ttm170) cc_final: 0.9045 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9221 (tm-30)
REVERT: D   17 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7037 (p90)
REVERT: D   48 GLU cc_start: 0.9123 (tp30) cc_final: 0.8617 (tm-30)
REVERT: D  100 MET cc_start: 0.9414 (ttp) cc_final: 0.9209 (ppp)
REVERT: D  101 ARG cc_start: 0.9424 (ttm170) cc_final: 0.9152 (ttp-110)
REVERT: D  213 MET cc_start: 0.9221 (mmm) cc_final: 0.8970 (mmp)
REVERT: D  224 ASN cc_start: 0.8899 (m-40) cc_final: 0.8521 (m110)
REVERT: D  227 GLU cc_start: 0.9431 (tm-30) cc_final: 0.9183 (tm-30)
REVERT: E   17 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7670 (p90)
REVERT: E   48 GLU cc_start: 0.9211 (tp30) cc_final: 0.8693 (tm-30)
REVERT: E  101 ARG cc_start: 0.9402 (ttm170) cc_final: 0.9059 (ttp-110)
REVERT: E  213 MET cc_start: 0.9195 (mmm) cc_final: 0.8908 (mmp)
REVERT: E  224 ASN cc_start: 0.9092 (m-40) cc_final: 0.8666 (m110)
REVERT: E  227 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9040 (tm-30)
REVERT: F   17 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7738 (p90)
REVERT: F   48 GLU cc_start: 0.9167 (tp30) cc_final: 0.8680 (tm-30)
REVERT: F  100 MET cc_start: 0.9346 (ttp) cc_final: 0.9104 (ppp)
REVERT: F  101 ARG cc_start: 0.9417 (ttm170) cc_final: 0.9040 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9216 (tm-30)
  outliers start: 54
  outliers final: 34
  residues processed: 220
  average time/residue: 0.1838
  time to fit residues: 59.4503
Evaluate side-chains
  213 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 173
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  228 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain E residue  228 LEU
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  228 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 104 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0970
   chunk 28 optimal weight:    9.9990
   chunk 116 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10218  Z= 0.173
  Angle     :  0.673   8.328  13824  Z= 0.342
  Chirality :  0.040   0.175   1572
  Planarity :  0.004   0.032   1662
  Dihedral  :  6.123  54.160   1334
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 26.05 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.25), residues: 1200
  helix:  1.67 (0.19), residues: 822
  sheet:  3.09 (0.65), residues: 66
  loop : -1.92 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP E  25 
 HIS   0.002   0.001   HIS E  74 
 PHE   0.019   0.001   PHE E  30 
 TYR   0.016   0.001   TYR E  92 
 ARG   0.004   0.000   ARG C  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 189
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7362 (p90)
REVERT: A   48 GLU cc_start: 0.9110 (tp30) cc_final: 0.8666 (tm-30)
REVERT: A  100 MET cc_start: 0.9386 (ttp) cc_final: 0.9140 (ppp)
REVERT: A  101 ARG cc_start: 0.9453 (ttm170) cc_final: 0.9078 (ttp-110)
REVERT: A  213 MET cc_start: 0.9140 (mmm) cc_final: 0.8852 (mmp)
REVERT: A  227 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9099 (tm-30)
REVERT: B   17 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7490 (p90)
REVERT: B   48 GLU cc_start: 0.9152 (tp30) cc_final: 0.8809 (tm-30)
REVERT: B  101 ARG cc_start: 0.9517 (ttm170) cc_final: 0.9047 (ttp-110)
REVERT: B  213 MET cc_start: 0.9169 (mmm) cc_final: 0.8963 (mmp)
REVERT: B  224 ASN cc_start: 0.9093 (m-40) cc_final: 0.8671 (m110)
REVERT: B  227 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9018 (tm-30)
REVERT: C   17 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7527 (p90)
REVERT: C   47 ASP cc_start: 0.8676 (p0) cc_final: 0.8461 (p0)
REVERT: C   48 GLU cc_start: 0.9099 (tp30) cc_final: 0.8754 (tm-30)
REVERT: C  100 MET cc_start: 0.9354 (ttp) cc_final: 0.9112 (ppp)
REVERT: C  101 ARG cc_start: 0.9417 (ttm170) cc_final: 0.9036 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9201 (tm-30)
REVERT: D   17 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.6899 (p90)
REVERT: D   42 GLU cc_start: 0.8492 (pp20) cc_final: 0.8260 (pp20)
REVERT: D   48 GLU cc_start: 0.9025 (tp30) cc_final: 0.8640 (tm-30)
REVERT: D  101 ARG cc_start: 0.9424 (ttm170) cc_final: 0.9157 (ptm-80)
REVERT: D  213 MET cc_start: 0.9194 (mmm) cc_final: 0.8936 (mmp)
REVERT: D  224 ASN cc_start: 0.8864 (m-40) cc_final: 0.8484 (m110)
REVERT: D  227 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9156 (tm-30)
REVERT: E   17 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7496 (p90)
REVERT: E   48 GLU cc_start: 0.9121 (tp30) cc_final: 0.8688 (tm-30)
REVERT: E  101 ARG cc_start: 0.9518 (ttm170) cc_final: 0.9043 (ttp-110)
REVERT: E  197 ASP cc_start: 0.8348 (t0) cc_final: 0.8043 (t0)
REVERT: E  213 MET cc_start: 0.9170 (mmm) cc_final: 0.8962 (mmp)
REVERT: E  224 ASN cc_start: 0.9095 (m-40) cc_final: 0.8672 (m110)
REVERT: E  227 GLU cc_start: 0.9413 (tm-30) cc_final: 0.9015 (tm-30)
REVERT: F   17 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7501 (p90)
REVERT: F  100 MET cc_start: 0.9353 (ttp) cc_final: 0.9111 (ppp)
REVERT: F  101 ARG cc_start: 0.9414 (ttm170) cc_final: 0.9035 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9201 (tm-30)
  outliers start: 41
  outliers final: 26
  residues processed: 218
  average time/residue: 0.1876
  time to fit residues: 59.2601
Evaluate side-chains
  210 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   30 PHE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   61 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  187 CYS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   30 PHE
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  171 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 84 optimal weight:    0.1980
   chunk 65 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 70 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10218  Z= 0.169
  Angle     :  0.663   8.520  13824  Z= 0.338
  Chirality :  0.040   0.175   1572
  Planarity :  0.004   0.033   1662
  Dihedral  :  5.852  55.726   1332
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 27.50 %
    Favored  : 68.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.25), residues: 1200
  helix:  1.60 (0.19), residues: 828
  sheet:  3.42 (0.66), residues: 66
  loop : -1.79 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  25 
 HIS   0.002   0.001   HIS B  74 
 PHE   0.025   0.001   PHE B  30 
 TYR   0.017   0.001   TYR D  92 
 ARG   0.004   0.000   ARG C  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 188
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7495 (p90)
REVERT: A  100 MET cc_start: 0.9373 (ttp) cc_final: 0.9133 (ppp)
REVERT: A  101 ARG cc_start: 0.9453 (ttm170) cc_final: 0.9118 (ptm-80)
REVERT: A  213 MET cc_start: 0.9150 (mmm) cc_final: 0.8870 (mmp)
REVERT: A  227 GLU cc_start: 0.9467 (tm-30) cc_final: 0.9169 (tm-30)
REVERT: B   17 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7332 (p90)
REVERT: B   48 GLU cc_start: 0.9101 (tp30) cc_final: 0.8812 (tm-30)
REVERT: B  101 ARG cc_start: 0.9519 (ttm170) cc_final: 0.9068 (ttp-110)
REVERT: B  213 MET cc_start: 0.9140 (mmm) cc_final: 0.8846 (mmp)
REVERT: B  224 ASN cc_start: 0.9154 (m-40) cc_final: 0.8684 (m110)
REVERT: B  227 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9012 (tm-30)
REVERT: C   17 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7461 (p90)
REVERT: C  100 MET cc_start: 0.9351 (ttp) cc_final: 0.9117 (ppp)
REVERT: C  101 ARG cc_start: 0.9416 (ttm170) cc_final: 0.9033 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9211 (tm-30)
REVERT: D   17 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7092 (p90)
REVERT: D   42 GLU cc_start: 0.8491 (pp20) cc_final: 0.8262 (mt-10)
REVERT: D   48 GLU cc_start: 0.9015 (tp30) cc_final: 0.8660 (tm-30)
REVERT: D  101 ARG cc_start: 0.9581 (ttm170) cc_final: 0.9133 (ttp-110)
REVERT: D  213 MET cc_start: 0.9192 (mmm) cc_final: 0.8957 (mmp)
REVERT: D  224 ASN cc_start: 0.8866 (m-40) cc_final: 0.8480 (m110)
REVERT: D  227 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9157 (tm-30)
REVERT: E   17 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7340 (p90)
REVERT: E   48 GLU cc_start: 0.9097 (tp30) cc_final: 0.8697 (tm-30)
REVERT: E  101 ARG cc_start: 0.9518 (ttm170) cc_final: 0.9058 (ttp-110)
REVERT: E  197 ASP cc_start: 0.8297 (t0) cc_final: 0.7998 (t0)
REVERT: E  213 MET cc_start: 0.9154 (mmm) cc_final: 0.8850 (mmp)
REVERT: E  224 ASN cc_start: 0.9170 (m-40) cc_final: 0.8694 (m110)
REVERT: E  227 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9010 (tm-30)
REVERT: F   17 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7461 (p90)
REVERT: F   47 ASP cc_start: 0.8676 (p0) cc_final: 0.8474 (p0)
REVERT: F   48 GLU cc_start: 0.9116 (tp30) cc_final: 0.8784 (tm-30)
REVERT: F  100 MET cc_start: 0.9356 (ttp) cc_final: 0.9123 (ppp)
REVERT: F  101 ARG cc_start: 0.9416 (ttm170) cc_final: 0.9032 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9211 (tm-30)
  outliers start: 45
  outliers final: 26
  residues processed: 221
  average time/residue: 0.1879
  time to fit residues: 60.9434
Evaluate side-chains
  212 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 180
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  171 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0470
   chunk 105 optimal weight:    8.9990
   overall best weight:    2.2086

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

Flipped N/Q/H residues before XYZ refinement:
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10218  Z= 0.214
  Angle     :  0.692   9.895  13824  Z= 0.354
  Chirality :  0.039   0.168   1572
  Planarity :  0.004   0.036   1662
  Dihedral  :  5.563  51.257   1328
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 27.50 %
    Favored  : 68.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1200
  helix:  1.63 (0.19), residues: 828
  sheet:  3.35 (0.66), residues: 66
  loop : -1.74 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  25 
 HIS   0.002   0.001   HIS D  74 
 PHE   0.030   0.001   PHE E  30 
 TYR   0.018   0.001   TYR D  92 
 ARG   0.003   0.000   ARG F  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 179
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7386 (p90)
REVERT: A  100 MET cc_start: 0.9378 (ttp) cc_final: 0.9149 (ppp)
REVERT: A  101 ARG cc_start: 0.9448 (ttm170) cc_final: 0.9073 (ttp-110)
REVERT: A  213 MET cc_start: 0.9181 (mmm) cc_final: 0.8907 (mmp)
REVERT: A  227 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9182 (tm-30)
REVERT: B   17 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7479 (p90)
REVERT: B   48 GLU cc_start: 0.9096 (tp30) cc_final: 0.8783 (tm-30)
REVERT: B  101 ARG cc_start: 0.9520 (ttm170) cc_final: 0.9068 (ttp-110)
REVERT: B  213 MET cc_start: 0.9161 (mmm) cc_final: 0.8881 (mmp)
REVERT: B  224 ASN cc_start: 0.9117 (m-40) cc_final: 0.8696 (m110)
REVERT: B  227 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9036 (tm-30)
REVERT: C   17 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7588 (p90)
REVERT: C   48 GLU cc_start: 0.9142 (tp30) cc_final: 0.8831 (tm-30)
REVERT: C  100 MET cc_start: 0.9344 (ttp) cc_final: 0.9123 (ppp)
REVERT: C  101 ARG cc_start: 0.9419 (ttm170) cc_final: 0.9038 (ttp-110)
REVERT: C  227 GLU cc_start: 0.9452 (tm-30) cc_final: 0.9239 (tm-30)
REVERT: D   17 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7027 (p90)
REVERT: D   42 GLU cc_start: 0.8515 (pp20) cc_final: 0.7969 (pm20)
REVERT: D   48 GLU cc_start: 0.9050 (tp30) cc_final: 0.8653 (tm-30)
REVERT: D  101 ARG cc_start: 0.9596 (ttm170) cc_final: 0.9151 (ttp-110)
REVERT: D  213 MET cc_start: 0.9191 (mmm) cc_final: 0.8966 (mmp)
REVERT: D  227 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9164 (tm-30)
REVERT: E   17 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7489 (p90)
REVERT: E   48 GLU cc_start: 0.9085 (tp30) cc_final: 0.8715 (tm-30)
REVERT: E  101 ARG cc_start: 0.9521 (ttm170) cc_final: 0.9066 (ttp-110)
REVERT: E  197 ASP cc_start: 0.8332 (t0) cc_final: 0.8006 (t0)
REVERT: E  213 MET cc_start: 0.9172 (mmm) cc_final: 0.8882 (mmp)
REVERT: E  224 ASN cc_start: 0.9122 (m-40) cc_final: 0.8707 (m110)
REVERT: E  227 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9018 (tm-30)
REVERT: F   17 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7571 (p90)
REVERT: F   48 GLU cc_start: 0.9120 (tp30) cc_final: 0.8803 (tm-30)
REVERT: F  100 MET cc_start: 0.9349 (ttp) cc_final: 0.9127 (ppp)
REVERT: F  101 ARG cc_start: 0.9417 (ttm170) cc_final: 0.9031 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9223 (tm-30)
  outliers start: 39
  outliers final: 23
  residues processed: 205
  average time/residue: 0.1955
  time to fit residues: 58.3341
Evaluate side-chains
  208 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 179
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   30 PHE
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   30 PHE
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  218 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 101 optimal weight:   10.0000
   chunk 107 optimal weight:    0.1980
   chunk 64 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0030
   chunk 113 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0030
   overall best weight:    0.2800

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

Flipped N/Q/H residues before XYZ refinement:
D  15 GLN
D  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.3980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10218  Z= 0.173
  Angle     :  0.721   9.667  13824  Z= 0.361
  Chirality :  0.040   0.172   1572
  Planarity :  0.004   0.033   1662
  Dihedral  :  5.418  48.717   1328
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 29.23 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.25), residues: 1200
  helix:  1.50 (0.19), residues: 834
  sheet:  3.49 (0.66), residues: 66
  loop : -1.73 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  25 
 HIS   0.002   0.001   HIS A  74 
 PHE   0.032   0.001   PHE E  30 
 TYR   0.017   0.001   TYR A  92 
 ARG   0.003   0.000   ARG C  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 186
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7200 (p90)
REVERT: A  100 MET cc_start: 0.9389 (ttp) cc_final: 0.9175 (ppp)
REVERT: A  101 ARG cc_start: 0.9434 (ttm170) cc_final: 0.9106 (ptm-80)
REVERT: A  213 MET cc_start: 0.9157 (mmm) cc_final: 0.8879 (mmp)
REVERT: A  227 GLU cc_start: 0.9474 (tm-30) cc_final: 0.9184 (tm-30)
REVERT: B   17 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7320 (p90)
REVERT: B   48 GLU cc_start: 0.9038 (tp30) cc_final: 0.8796 (tm-30)
REVERT: B  101 ARG cc_start: 0.9515 (ttm170) cc_final: 0.9065 (ttp-110)
REVERT: B  213 MET cc_start: 0.9137 (mmm) cc_final: 0.8843 (mmp)
REVERT: B  224 ASN cc_start: 0.9046 (m-40) cc_final: 0.8647 (m110)
REVERT: B  227 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9006 (tm-30)
REVERT: C   17 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7363 (p90)
REVERT: C  100 MET cc_start: 0.9353 (ttp) cc_final: 0.9135 (ppp)
REVERT: C  101 ARG cc_start: 0.9411 (ttm170) cc_final: 0.9054 (ptm-80)
REVERT: C  227 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9232 (tm-30)
REVERT: D   17 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7221 (p90)
REVERT: D   48 GLU cc_start: 0.8997 (tp30) cc_final: 0.8697 (tm-30)
REVERT: D  101 ARG cc_start: 0.9586 (ttm170) cc_final: 0.9131 (ttp-110)
REVERT: D  213 MET cc_start: 0.9170 (mmm) cc_final: 0.8912 (mmp)
REVERT: D  227 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9146 (tm-30)
REVERT: E   17 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7231 (p90)
REVERT: E   48 GLU cc_start: 0.9013 (tp30) cc_final: 0.8737 (tm-30)
REVERT: E  101 ARG cc_start: 0.9518 (ttm170) cc_final: 0.9068 (ttp-110)
REVERT: E  197 ASP cc_start: 0.8331 (t0) cc_final: 0.7999 (t0)
REVERT: E  213 MET cc_start: 0.9140 (mmm) cc_final: 0.8842 (mmp)
REVERT: E  224 ASN cc_start: 0.9048 (m-40) cc_final: 0.8653 (m110)
REVERT: E  227 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9011 (tm-30)
REVERT: F   17 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.7367 (p90)
REVERT: F   48 GLU cc_start: 0.9027 (tp30) cc_final: 0.8812 (tm-30)
REVERT: F  100 MET cc_start: 0.9350 (ttp) cc_final: 0.9135 (ppp)
REVERT: F  101 ARG cc_start: 0.9409 (ttm170) cc_final: 0.9015 (ttp-110)
REVERT: F  227 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9200 (tm-30)
  outliers start: 29
  outliers final: 18
  residues processed: 207
  average time/residue: 0.1920
  time to fit residues: 58.5036
Evaluate side-chains
  201 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 177
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 119 optimal weight:    4.9990
   chunk 110 optimal weight:   20.0000
   chunk 95 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.7188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.4017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10218  Z= 0.202
  Angle     :  0.721  10.188  13824  Z= 0.369
  Chirality :  0.039   0.177   1572
  Planarity :  0.004   0.034   1662
  Dihedral  :  5.469  49.281   1328
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 29.33 %
    Favored  : 68.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1200
  helix:  1.50 (0.19), residues: 834
  sheet:  3.55 (0.66), residues: 66
  loop : -1.60 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.001   TRP D  25 
 HIS   0.002   0.001   HIS D  74 
 PHE   0.035   0.001   PHE B  30 
 TYR   0.018   0.001   TYR A  92 
 ARG   0.002   0.000   ARG F  53 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 177
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7282 (p90)
REVERT: A  101 ARG cc_start: 0.9436 (ttm170) cc_final: 0.9095 (ptm-80)
REVERT: A  213 MET cc_start: 0.9160 (mmm) cc_final: 0.8902 (mmp)
REVERT: A  227 GLU cc_start: 0.9473 (tm-30) cc_final: 0.9195 (tm-30)
REVERT: B   17 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7354 (p90)
REVERT: B   48 GLU cc_start: 0.9081 (tp30) cc_final: 0.8817 (tm-30)
REVERT: B  101 ARG cc_start: 0.9521 (ttm170) cc_final: 0.9088 (ttp-110)
REVERT: B  213 MET cc_start: 0.9146 (mmm) cc_final: 0.8882 (mmp)
REVERT: B  224 ASN cc_start: 0.9048 (m-40) cc_final: 0.8677 (m110)
REVERT: B  227 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9032 (tm-30)
REVERT: C   17 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7429 (p90)
REVERT: C  100 MET cc_start: 0.9345 (ttp) cc_final: 0.9136 (ppp)
REVERT: C  101 ARG cc_start: 0.9418 (ttm170) cc_final: 0.9115 (ttp80)
REVERT: C  227 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9236 (tm-30)
REVERT: D   17 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7213 (p90)
REVERT: D   48 GLU cc_start: 0.8974 (tp30) cc_final: 0.8664 (tm-30)
REVERT: D  101 ARG cc_start: 0.9580 (ttm170) cc_final: 0.9135 (ttp-110)
REVERT: D  213 MET cc_start: 0.9191 (mmm) cc_final: 0.8962 (mmp)
REVERT: D  227 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9170 (tm-30)
REVERT: E   17 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7358 (p90)
REVERT: E   48 GLU cc_start: 0.9055 (tp30) cc_final: 0.8745 (tm-30)
REVERT: E  101 ARG cc_start: 0.9526 (ttm170) cc_final: 0.9084 (ttp-110)
REVERT: E  197 ASP cc_start: 0.8371 (t0) cc_final: 0.8034 (t0)
REVERT: E  213 MET cc_start: 0.9160 (mmm) cc_final: 0.8883 (mmp)
REVERT: E  224 ASN cc_start: 0.9051 (m-40) cc_final: 0.8684 (m110)
REVERT: E  227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9032 (tm-30)
REVERT: F   17 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7432 (p90)
REVERT: F   48 GLU cc_start: 0.9052 (tp30) cc_final: 0.8792 (tm-30)
REVERT: F  100 MET cc_start: 0.9341 (ttp) cc_final: 0.9128 (ppp)
REVERT: F  101 ARG cc_start: 0.9416 (ttm170) cc_final: 0.9110 (ttp80)
REVERT: F  227 GLU cc_start: 0.9442 (tm-30) cc_final: 0.9231 (tm-30)
  outliers start: 29
  outliers final: 18
  residues processed: 201
  average time/residue: 0.1978
  time to fit residues: 57.8351
Evaluate side-chains
  198 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain C residue   17 TYR
Chi-restraints excluded: chain C residue   26 LEU
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain D residue   17 TYR
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue   17 TYR
Chi-restraints excluded: chain E residue   65 CYS
Chi-restraints excluded: chain E residue   67 ASP
Chi-restraints excluded: chain E residue  198 CYS
Chi-restraints excluded: chain F residue   17 TYR
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   65 CYS
Chi-restraints excluded: chain F residue   67 ASP
Chi-restraints excluded: chain F residue   87 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 97 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.056648 restraints weight = 41264.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.058434 restraints weight = 19198.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.059565 restraints weight = 12218.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10218  Z= 0.182
  Angle     :  0.727  11.818  13824  Z= 0.370
  Chirality :  0.040   0.164   1572
  Planarity :  0.004   0.035   1662
  Dihedral  :  5.394  48.202   1328
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 29.33 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.26), residues: 1200
  helix:  1.58 (0.19), residues: 822
  sheet:  3.64 (0.67), residues: 66
  loop : -1.34 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP A  25 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.035   0.001   PHE E  30 
 TYR   0.017   0.001   TYR E  92 
 ARG   0.003   0.000   ARG A 101 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1945.00 seconds
wall clock time: 36 minutes 46.65 seconds (2206.65 seconds total)