Starting phenix.real_space_refine
on Wed Feb 12 07:09:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9imh_60689/02_2025/9imh_60689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9imh_60689/02_2025/9imh_60689.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9imh_60689/02_2025/9imh_60689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9imh_60689/02_2025/9imh_60689.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9imh_60689/02_2025/9imh_60689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9imh_60689/02_2025/9imh_60689.cif"
  }
  resolution = 4.2
  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
-------------------------------------------------------------------------------
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=   0.003 sd=   0.855
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      36      5.16       5
     C    4842      2.51       5
     N    1272      2.21       5
     O    1524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7674
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1290
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 9, 'TRANS': 151}
    Chain: "B"
      Number of atoms: 1268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1268
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 9, 'TRANS': 149}
    Chain: "C"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1290
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 9, 'TRANS': 151}
    Chain: "D"
      Number of atoms: 1268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1268
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 9, 'TRANS': 149}
    Chain: "E"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1290
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 9, 'TRANS': 151}
    Chain: "F"
      Number of atoms: 1268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1268
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 9, 'TRANS': 149}
  Time building chain proxies: 4.84, per 1000 atoms: 0.63
  Number of scatterers: 7674
  At special positions: 0
  Unit cell: (111.8, 107.9, 61.1, 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      36     16.00
     O    1524      8.00
     N    1272      7.00
     C    4842      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.12
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1800

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 14 sheets defined
      23.1% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 19
    Processing helix  chain 'A' and resid 85 through 103
    Processing helix  chain 'B' and resid 3 through 20
    Processing helix  chain 'B' and resid 85 through 103
    Processing helix  chain 'C' and resid 3 through 20
      removed outlier: 3.564A  pdb=" N   ASP C  20 " --> pdb=" O   SER C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 103
    Processing helix  chain 'D' and resid 3 through 20
    Processing helix  chain 'D' and resid 85 through 103
    Processing helix  chain 'E' and resid 3 through 20
    Processing helix  chain 'E' and resid 85 through 104
      removed outlier: 3.623A  pdb=" N   GLN E  89 " --> pdb=" O   ASP E  85 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLY E 104 " --> pdb=" O   VAL E 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 20
      removed outlier: 3.503A  pdb=" N   ILE F   7 " --> pdb=" O   HIS F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 85 through 103
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53
      removed outlier: 3.983A  pdb=" N   MET A  70 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR A 152 " --> pdb=" O   MET A  70 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 148 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   GLU A 145 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   VAL A 131 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ASN A 147 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 53
      removed outlier: 3.546A  pdb=" N   TRP B  69 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 53
      removed outlier: 3.543A  pdb=" N   MET B  70 " --> pdb=" O   TYR B 152 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TYR B 152 " --> pdb=" O   MET B  70 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL B 148 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   GLU B 145 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   VAL B 131 " --> pdb=" O   GLU B 145 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ASN B 147 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ARG B 151 " --> pdb=" O   ASP B 125 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP B 125 " --> pdb=" O   ARG B 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109
    Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 53
    Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 53
      removed outlier: 3.658A  pdb=" N   MET C  70 " --> pdb=" O   TYR C 152 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TYR C 152 " --> pdb=" O   MET C  70 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LEU C 143 " --> pdb=" O   THR C 133 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   THR C 133 " --> pdb=" O   LEU C 143 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   GLU C 145 " --> pdb=" O   VAL C 131 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   VAL C 131 " --> pdb=" O   GLU C 145 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ASN C 147 " --> pdb=" O   THR C 129 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 53
    Processing sheet with id=AA9, first strand: chain 'D' and resid 51 through 53
      removed outlier: 3.594A  pdb=" N   MET D  70 " --> pdb=" O   TYR D 152 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   TYR D 152 " --> pdb=" O   MET D  70 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL D 148 " --> pdb=" O   LEU D  74 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   GLU D 145 " --> pdb=" O   VAL D 131 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   VAL D 131 " --> pdb=" O   GLU D 145 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   ASN D 147 " --> pdb=" O   THR D 129 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 51 through 53
    Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 53
      removed outlier: 3.633A  pdb=" N   MET E  70 " --> pdb=" O   TYR E 152 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL E 148 " --> pdb=" O   LEU E  74 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   ASN E 147 " --> pdb=" O   THR E 129 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 107 through 108
      removed outlier: 4.531A  pdb=" N   LEU E 107 " --> pdb=" O   ALA E 123 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 53
      removed outlier: 3.510A  pdb=" N   TRP F  69 " --> pdb=" O   GLN F  61 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 51 through 53
      removed outlier: 3.698A  pdb=" N   TYR F 152 " --> pdb=" O   MET F  70 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL F 148 " --> pdb=" O   LEU F  74 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL F  78 " --> pdb=" O   ALA F 144 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA F 144 " --> pdb=" O   VAL F  78 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   GLU F 145 " --> pdb=" O   VAL F 131 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   VAL F 131 " --> pdb=" O   GLU F 145 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ASN F 147 " --> pdb=" O   THR F 129 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    837 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: 2.03

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1335
        1.31 -     1.44: 2014
        1.44 -     1.56: 4415
        1.56 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 7830
  Sorted by residual:
  bond pdb=" CA  TYR A  50 "
       pdb=" C   TYR A  50 "
    ideal  model  delta    sigma   weight residual
    1.524  1.441  0.083 1.27e-02 6.20e+03 4.22e+01
  bond pdb=" CA  PHE A  48 "
       pdb=" CB  PHE A  48 "
    ideal  model  delta    sigma   weight residual
    1.530  1.439  0.091 1.58e-02 4.01e+03 3.33e+01
  bond pdb=" CA  PHE B  48 "
       pdb=" CB  PHE B  48 "
    ideal  model  delta    sigma   weight residual
    1.530  1.443  0.087 1.58e-02 4.01e+03 3.05e+01
  bond pdb=" CA  GLU D  47 "
       pdb=" C   GLU D  47 "
    ideal  model  delta    sigma   weight residual
    1.524  1.465  0.059 1.31e-02 5.83e+03 2.06e+01
  bond pdb=" CA  PRO E  49 "
       pdb=" CB  PRO E  49 "
    ideal  model  delta    sigma   weight residual
    1.533  1.469  0.064 1.42e-02 4.96e+03 2.04e+01
  ... (remaining 7825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 10364
        3.04 -     6.09: 214
        6.09 -     9.13: 43
        9.13 -    12.18: 4
       12.18 -    15.22: 1
  Bond angle restraints: 10626
  Sorted by residual:
  angle pdb=" N   PHE D  28 "
        pdb=" CA  PHE D  28 "
        pdb=" C   PHE D  28 "
      ideal   model   delta    sigma   weight residual
     107.62  122.84  -15.22 1.97e+00 2.58e-01 5.97e+01
  angle pdb=" C   GLU D  82 "
        pdb=" CA  GLU D  82 "
        pdb=" CB  GLU D  82 "
      ideal   model   delta    sigma   weight residual
     117.23  107.87    9.36 1.36e+00 5.41e-01 4.74e+01
  angle pdb=" CA  GLU D  82 "
        pdb=" C   GLU D  82 "
        pdb=" N   LYS D  83 "
      ideal   model   delta    sigma   weight residual
     119.98  114.84    5.14 8.50e-01 1.38e+00 3.66e+01
  angle pdb=" C   PRO C  49 "
        pdb=" N   TYR C  50 "
        pdb=" CA  TYR C  50 "
      ideal   model   delta    sigma   weight residual
     122.19  130.29   -8.10 1.41e+00 5.03e-01 3.30e+01
  angle pdb=" CA  PRO F  49 "
        pdb=" N   PRO F  49 "
        pdb=" CD  PRO F  49 "
      ideal   model   delta    sigma   weight residual
     112.00  104.68    7.32 1.40e+00 5.10e-01 2.73e+01
  ... (remaining 10621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4217
       17.88 -    35.76: 424
       35.76 -    53.64: 100
       53.64 -    71.52: 14
       71.52 -    89.41: 9
  Dihedral angle restraints: 4764
    sinusoidal: 1956
      harmonic: 2808
  Sorted by residual:
  dihedral pdb=" C   PHE D  48 "
           pdb=" N   PHE D  48 "
           pdb=" CA  PHE D  48 "
           pdb=" CB  PHE D  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -148.93   26.33     0      2.50e+00 1.60e-01 1.11e+02
  dihedral pdb=" N   PHE D  48 "
           pdb=" C   PHE D  48 "
           pdb=" CA  PHE D  48 "
           pdb=" CB  PHE D  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  147.16  -24.36     0      2.50e+00 1.60e-01 9.50e+01
  dihedral pdb=" C   PHE F  48 "
           pdb=" N   PHE F  48 "
           pdb=" CA  PHE F  48 "
           pdb=" CB  PHE F  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.98   19.38     0      2.50e+00 1.60e-01 6.01e+01
  ... (remaining 4761 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.232: 1171
       0.232 -    0.465: 4
       0.465 -    0.697: 4
       0.697 -    0.929: 2
       0.929 -    1.161: 1
  Chirality restraints: 1182
  Sorted by residual:
  chirality pdb=" CA  PHE D  48 "
            pdb=" N   PHE D  48 "
            pdb=" C   PHE D  48 "
            pdb=" CB  PHE D  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.35    1.16 2.00e-01 2.50e+01 3.37e+01
  chirality pdb=" CA  PHE F  48 "
            pdb=" N   PHE F  48 "
            pdb=" C   PHE F  48 "
            pdb=" CB  PHE F  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.70    0.81 2.00e-01 2.50e+01 1.64e+01
  chirality pdb=" CA  PHE B  48 "
            pdb=" N   PHE B  48 "
            pdb=" C   PHE B  48 "
            pdb=" CB  PHE B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.78    0.73 2.00e-01 2.50e+01 1.34e+01
  ... (remaining 1179 not shown)

  Planarity restraints: 1392
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE F  48 "    0.106 5.00e-02 4.00e+02   1.57e-01 3.95e+01
        pdb=" N   PRO F  49 "   -0.272 5.00e-02 4.00e+02
        pdb=" CA  PRO F  49 "    0.085 5.00e-02 4.00e+02
        pdb=" CD  PRO F  49 "    0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D  48 "   -0.101 5.00e-02 4.00e+02   1.54e-01 3.78e+01
        pdb=" N   PRO D  49 "    0.266 5.00e-02 4.00e+02
        pdb=" CA  PRO D  49 "   -0.084 5.00e-02 4.00e+02
        pdb=" CD  PRO D  49 "   -0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C  48 "   -0.096 5.00e-02 4.00e+02   1.47e-01 3.44e+01
        pdb=" N   PRO C  49 "    0.254 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "   -0.082 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "   -0.075 5.00e-02 4.00e+02
  ... (remaining 1389 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 445
        2.72 -     3.26: 7800
        3.26 -     3.81: 11681
        3.81 -     4.35: 13461
        4.35 -     4.90: 22994
  Nonbonded interactions: 56381
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  84 "
            pdb=" N   ASP D  85 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" O   THR B  39 "
            pdb=" OH  TYR B  50 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   THR D  39 "
            pdb=" OH  TYR D  50 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   LYS E  83 "
            pdb=" OG1 THR E  84 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   THR A  99 "
            pdb=" OG1 THR A 103 "
     model   vdw
     2.256 3.040
  ... (remaining 56376 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 1 through 159)
  selection = chain 'B'
  selection = (chain 'C' and resid 1 through 159)
  selection = chain 'D'
  selection = (chain 'E' and resid 1 through 159)
  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:             9.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     20.090
  Find NCS groups from input model:        0.370
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
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      :  0.006   0.091   7830  Z= 0.346
  Angle     :  1.059  15.223  10626  Z= 0.596
  Chirality :  0.078   1.161   1182
  Planarity :  0.011   0.157   1392
  Dihedral  : 15.415  89.406   2964
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 19.62
  Ramachandran Plot:
    Outliers :  3.48 %
    Allowed  : 12.03 %
    Favored  : 84.49 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  0.93 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.78 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.28), residues: 948
  helix:  0.75 (0.38), residues: 198
  sheet: -0.50 (0.29), residues: 333
  loop : -3.35 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  69 
 HIS   0.004   0.001   HIS D   3 
 PHE   0.029   0.002   PHE D  28 
 TYR   0.038   0.002   TYR B 109 
 ARG   0.005   0.000   ARG D 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 319
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7087 (m-40) cc_final: 0.6794 (m-40)
REVERT: A   80 ASP cc_start: 0.7572 (t0) cc_final: 0.6350 (t0)
REVERT: B   70 MET cc_start: 0.7965 (tpp) cc_final: 0.7541 (mtt)
REVERT: B   88 GLU cc_start: 0.7151 (tp30) cc_final: 0.6905 (tm-30)
REVERT: B  113 LYS cc_start: 0.6787 (tppt) cc_final: 0.6368 (tmmt)
REVERT: C   45 ILE cc_start: 0.9069 (mp) cc_final: 0.8605 (mt)
REVERT: C   69 TRP cc_start: 0.8906 (m100) cc_final: 0.8128 (m100)
REVERT: D   46 ARG cc_start: 0.7385 (mpt90) cc_final: 0.5666 (ttt180)
REVERT: E   29 ASN cc_start: 0.6881 (m110) cc_final: 0.6430 (m110)
REVERT: E   45 ILE cc_start: 0.8224 (mm) cc_final: 0.7902 (tp)
REVERT: F    3 HIS cc_start: 0.6935 (m170) cc_final: 0.6722 (m170)
REVERT: F   70 MET cc_start: 0.8554 (tpp) cc_final: 0.8209 (mmt)
REVERT: F   81 LYS cc_start: 0.7218 (ttpp) cc_final: 0.7017 (ttpt)
REVERT: F  108 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5663 (tp30)
  outliers start: 6
  outliers final: 4
  residues processed: 323
  average time/residue: 0.2027
  time to fit residues: 86.6654
Evaluate side-chains
  223 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 219
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 47 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 28 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A  68 GLN
B  34 ASN
C  29 ASN
C  38 GLN
D  34 ASN
D  87 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.128761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.120683 restraints weight = 15553.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.122966 restraints weight = 8881.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.124477 restraints weight = 5508.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   7830  Z= 0.321
  Angle     :  0.921  18.775  10626  Z= 0.466
  Chirality :  0.051   0.243   1182
  Planarity :  0.012   0.175   1392
  Dihedral  :  7.114  43.990   1056
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  2.43 %
    Allowed  : 12.13 %
    Favored  : 85.44 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.94 %
    Favored  : 93.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

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: -1.97 (0.27), residues: 948
  helix:  0.93 (0.37), residues: 198
  sheet: -0.25 (0.28), residues: 351
  loop : -3.61 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  69 
 HIS   0.006   0.001   HIS D   3 
 PHE   0.018   0.003   PHE E  71 
 TYR   0.037   0.002   TYR B 109 
 ARG   0.005   0.000   ARG D   4 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 272
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7060 (m110) cc_final: 0.6602 (m-40)
REVERT: A   85 ASP cc_start: 0.6560 (t0) cc_final: 0.5924 (t0)
REVERT: B   26 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.5701 (pm20)
REVERT: B   40 TYR cc_start: 0.7376 (p90) cc_final: 0.7168 (p90)
REVERT: B   70 MET cc_start: 0.8238 (tpp) cc_final: 0.7854 (mtt)
REVERT: B   88 GLU cc_start: 0.8002 (tp30) cc_final: 0.7170 (tm-30)
REVERT: B   92 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7529 (mmtp)
REVERT: C   45 ILE cc_start: 0.9006 (mp) cc_final: 0.8760 (mt)
REVERT: C   46 ARG cc_start: 0.7215 (ttt180) cc_final: 0.4841 (ttp80)
REVERT: C   80 ASP cc_start: 0.7799 (t0) cc_final: 0.7388 (t0)
REVERT: D   23 GLN cc_start: 0.7840 (pm20) cc_final: 0.7539 (pm20)
REVERT: D   46 ARG cc_start: 0.7442 (mpt90) cc_final: 0.5469 (ttt180)
REVERT: D  134 ASP cc_start: 0.8354 (p0) cc_final: 0.8138 (p0)
REVERT: E    1 MET cc_start: 0.7392 (ttm) cc_final: 0.6523 (mtp)
REVERT: E   29 ASN cc_start: 0.6763 (m110) cc_final: 0.6481 (m-40)
REVERT: E  141 TYR cc_start: 0.7861 (m-10) cc_final: 0.7428 (m-80)
REVERT: F    3 HIS cc_start: 0.7431 (m170) cc_final: 0.7183 (m170)
REVERT: F    6 SER cc_start: 0.8560 (m) cc_final: 0.8325 (p)
REVERT: F  108 GLU cc_start: 0.6463 (mm-30) cc_final: 0.6056 (tp30)
REVERT: F  134 ASP cc_start: 0.8589 (p0) cc_final: 0.8177 (p0)
  outliers start: 5
  outliers final: 3
  residues processed: 276
  average time/residue: 0.1896
  time to fit residues: 71.8785
Evaluate side-chains
  210 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 206
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    0.4980
   chunk 45 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0970
   chunk 63 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  89 GLN
C  29 ASN
D  89 GLN
E  68 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.131431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.123206 restraints weight = 15295.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.125582 restraints weight = 8503.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.127128 restraints weight = 5200.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089   7830  Z= 0.244
  Angle     :  0.869  19.587  10626  Z= 0.431
  Chirality :  0.049   0.231   1182
  Planarity :  0.012   0.180   1392
  Dihedral  :  6.803  43.825   1056
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  2.53 %
    Allowed  : 12.34 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  4.43 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    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: -1.62 (0.28), residues: 948
  helix:  1.14 (0.37), residues: 198
  sheet:  0.35 (0.31), residues: 291
  loop : -3.25 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F  69 
 HIS   0.008   0.001   HIS B   3 
 PHE   0.014   0.002   PHE A 119 
 TYR   0.026   0.002   TYR B 109 
 ARG   0.009   0.000   ARG C   4 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 285
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.8556 (ttt) cc_final: 0.8210 (ttt)
REVERT: A   29 ASN cc_start: 0.6765 (m110) cc_final: 0.6160 (m110)
REVERT: A   72 LEU cc_start: 0.8775 (tp) cc_final: 0.8563 (tt)
REVERT: A   74 LEU cc_start: 0.8964 (mp) cc_final: 0.8612 (mp)
REVERT: A   85 ASP cc_start: 0.7233 (t0) cc_final: 0.6860 (t0)
REVERT: B   17 LYS cc_start: 0.7082 (pttt) cc_final: 0.6661 (mmmt)
REVERT: B   40 TYR cc_start: 0.7124 (p90) cc_final: 0.6921 (p90)
REVERT: B   70 MET cc_start: 0.8251 (tpp) cc_final: 0.7818 (mtt)
REVERT: B   89 GLN cc_start: 0.7600 (tt0) cc_final: 0.7298 (tt0)
REVERT: C   29 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.6708 (m110)
REVERT: C   80 ASP cc_start: 0.7786 (t0) cc_final: 0.7420 (t0)
REVERT: C   91 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6815 (tm-30)
REVERT: C  122 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7203 (mm-30)
REVERT: D   22 SER cc_start: 0.8113 (p) cc_final: 0.7887 (p)
REVERT: D   29 ASN cc_start: 0.7931 (p0) cc_final: 0.7498 (p0)
REVERT: D   46 ARG cc_start: 0.7635 (mpt90) cc_final: 0.5218 (ttt180)
REVERT: D   47 GLU cc_start: 0.5941 (mp0) cc_final: 0.5448 (mp0)
REVERT: D  119 PHE cc_start: 0.6859 (m-80) cc_final: 0.6658 (m-80)
REVERT: E    1 MET cc_start: 0.7190 (ttm) cc_final: 0.6987 (mtp)
REVERT: E  141 TYR cc_start: 0.7849 (m-10) cc_final: 0.7423 (m-80)
REVERT: F    4 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7905 (ttp80)
REVERT: F   26 GLU cc_start: 0.7279 (pt0) cc_final: 0.6377 (mm-30)
REVERT: F   82 GLU cc_start: 0.6851 (mp0) cc_final: 0.6630 (mp0)
REVERT: F   88 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: F  108 GLU cc_start: 0.6341 (mm-30) cc_final: 0.5870 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 288
  average time/residue: 0.1820
  time to fit residues: 70.7408
Evaluate side-chains
  235 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 233
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 72 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0370
   chunk 66 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0570
   chunk 16 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.134461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.125756 restraints weight = 15237.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.128245 restraints weight = 8461.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.129838 restraints weight = 5186.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091   7830  Z= 0.228
  Angle     :  0.844  19.792  10626  Z= 0.414
  Chirality :  0.048   0.222   1182
  Planarity :  0.012   0.182   1392
  Dihedral  :  6.437  43.125   1056
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  2.53 %
    Allowed  : 11.71 %
    Favored  : 85.76 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.20 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

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: -1.34 (0.28), residues: 948
  helix:  1.32 (0.37), residues: 198
  sheet:  0.44 (0.32), residues: 279
  loop : -2.89 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP F  69 
 HIS   0.007   0.001   HIS B   3 
 PHE   0.017   0.002   PHE C 119 
 TYR   0.022   0.001   TYR B 109 
 ARG   0.007   0.000   ARG F 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 276
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.6742 (m110) cc_final: 0.6083 (m110)
REVERT: A   45 ILE cc_start: 0.8377 (mp) cc_final: 0.8076 (mt)
REVERT: A   74 LEU cc_start: 0.9034 (mp) cc_final: 0.8643 (mp)
REVERT: A  109 TYR cc_start: 0.6910 (m-10) cc_final: 0.6705 (m-10)
REVERT: B   17 LYS cc_start: 0.7000 (pttt) cc_final: 0.6647 (mmmt)
REVERT: B   40 TYR cc_start: 0.7114 (p90) cc_final: 0.6884 (p90)
REVERT: B   70 MET cc_start: 0.8292 (tpp) cc_final: 0.7842 (mtt)
REVERT: B   89 GLN cc_start: 0.7678 (tt0) cc_final: 0.7235 (tt0)
REVERT: B  132 SER cc_start: 0.8162 (t) cc_final: 0.7947 (t)
REVERT: C   29 ASN cc_start: 0.7182 (m110) cc_final: 0.6964 (m-40)
REVERT: C   80 ASP cc_start: 0.7915 (t0) cc_final: 0.7565 (t0)
REVERT: C   91 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6947 (tm-30)
REVERT: D   22 SER cc_start: 0.8102 (p) cc_final: 0.7850 (p)
REVERT: D   28 PHE cc_start: 0.7941 (p90) cc_final: 0.7578 (p90)
REVERT: D   46 ARG cc_start: 0.7703 (mpt90) cc_final: 0.5120 (ttt180)
REVERT: D   70 MET cc_start: 0.8267 (mmt) cc_final: 0.8004 (mmt)
REVERT: D   82 GLU cc_start: 0.7874 (mp0) cc_final: 0.7390 (mp0)
REVERT: D   91 GLU cc_start: 0.6932 (pp20) cc_final: 0.6698 (pp20)
REVERT: E    3 HIS cc_start: 0.7405 (m170) cc_final: 0.7151 (m170)
REVERT: F    4 ARG cc_start: 0.8136 (ptp90) cc_final: 0.7705 (ttm110)
REVERT: F   98 LYS cc_start: 0.8511 (tttt) cc_final: 0.7910 (ttmt)
REVERT: F  108 GLU cc_start: 0.6300 (mm-30) cc_final: 0.5871 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 277
  average time/residue: 0.1777
  time to fit residues: 67.2086
Evaluate side-chains
  227 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  38 GLN
C 147 ASN
D  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.127529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.119088 restraints weight = 15323.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.121501 restraints weight = 8556.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.123102 restraints weight = 5234.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084   7830  Z= 0.287
  Angle     :  0.885  21.432  10626  Z= 0.435
  Chirality :  0.050   0.259   1182
  Planarity :  0.012   0.186   1392
  Dihedral  :  6.648  43.183   1056
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  2.32 %
    Allowed  : 12.87 %
    Favored  : 84.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    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: -1.54 (0.28), residues: 948
  helix:  1.27 (0.37), residues: 198
  sheet: -0.07 (0.28), residues: 333
  loop : -3.11 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  69 
 HIS   0.005   0.001   HIS B   3 
 PHE   0.017   0.002   PHE E  48 
 TYR   0.023   0.002   TYR D 109 
 ARG   0.004   0.000   ARG F 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.7820 (mtp) cc_final: 0.7551 (mtm)
REVERT: A   29 ASN cc_start: 0.7085 (m110) cc_final: 0.6458 (m-40)
REVERT: B   17 LYS cc_start: 0.7228 (pttt) cc_final: 0.6925 (mmmt)
REVERT: B   40 TYR cc_start: 0.7562 (p90) cc_final: 0.7357 (p90)
REVERT: B   70 MET cc_start: 0.8265 (tpp) cc_final: 0.7977 (mtt)
REVERT: B   80 ASP cc_start: 0.7308 (m-30) cc_final: 0.7052 (m-30)
REVERT: B   88 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7378 (tm-30)
REVERT: B   91 GLU cc_start: 0.6864 (pp20) cc_final: 0.6487 (pp20)
REVERT: B  132 SER cc_start: 0.8178 (t) cc_final: 0.7938 (t)
REVERT: B  134 ASP cc_start: 0.8165 (p0) cc_final: 0.7711 (p0)
REVERT: C   29 ASN cc_start: 0.7186 (m110) cc_final: 0.6823 (m-40)
REVERT: C   80 ASP cc_start: 0.7711 (t0) cc_final: 0.7401 (t0)
REVERT: C   91 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7448 (tm-30)
REVERT: D   38 GLN cc_start: 0.7391 (mm-40) cc_final: 0.7188 (mm-40)
REVERT: D   46 ARG cc_start: 0.7565 (mpt90) cc_final: 0.5374 (ttt180)
REVERT: D   82 GLU cc_start: 0.8005 (mp0) cc_final: 0.7631 (mp0)
REVERT: D  132 SER cc_start: 0.9040 (m) cc_final: 0.8736 (p)
REVERT: E    1 MET cc_start: 0.7602 (mtp) cc_final: 0.7388 (mtp)
REVERT: E   70 MET cc_start: 0.8390 (mmm) cc_final: 0.8187 (mmm)
REVERT: F   82 GLU cc_start: 0.6900 (mp0) cc_final: 0.6576 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.1824
  time to fit residues: 62.4014
Evaluate side-chains
  208 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 75 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0770
   chunk 90 optimal weight:    5.9990
   chunk 11 optimal weight:    0.4980
   chunk 50 optimal weight:   10.0000
   chunk 69 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 153 GLN
D  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.132354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.124186 restraints weight = 15119.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.126540 restraints weight = 8291.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.128099 restraints weight = 5010.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   7830  Z= 0.228
  Angle     :  0.820  14.677  10626  Z= 0.410
  Chirality :  0.048   0.207   1182
  Planarity :  0.011   0.165   1392
  Dihedral  :  6.465  42.898   1056
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  2.11 %
    Allowed  : 12.34 %
    Favored  : 85.55 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.10 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    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: -1.37 (0.29), residues: 948
  helix:  1.25 (0.37), residues: 198
  sheet:  0.14 (0.29), residues: 315
  loop : -2.90 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  69 
 HIS   0.007   0.002   HIS E   3 
 PHE   0.012   0.002   PHE B  28 
 TYR   0.023   0.002   TYR F 109 
 ARG   0.006   0.000   ARG A   4 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 285
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.7586 (mtp) cc_final: 0.7341 (mtm)
REVERT: A   29 ASN cc_start: 0.6948 (m110) cc_final: 0.6343 (m-40)
REVERT: B   17 LYS cc_start: 0.7349 (ptmt) cc_final: 0.6766 (mmmt)
REVERT: B   29 ASN cc_start: 0.6808 (p0) cc_final: 0.6512 (p0)
REVERT: B   70 MET cc_start: 0.8281 (tpp) cc_final: 0.7936 (mtt)
REVERT: B   92 LYS cc_start: 0.7881 (mmtp) cc_final: 0.7340 (mmtm)
REVERT: B  132 SER cc_start: 0.7881 (t) cc_final: 0.7633 (t)
REVERT: C   80 ASP cc_start: 0.7761 (t0) cc_final: 0.7514 (t0)
REVERT: C   85 ASP cc_start: 0.6200 (t0) cc_final: 0.5884 (p0)
REVERT: C   91 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7177 (tm-30)
REVERT: C  141 TYR cc_start: 0.7362 (m-10) cc_final: 0.6941 (m-10)
REVERT: D   38 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7216 (mm-40)
REVERT: D   46 ARG cc_start: 0.7516 (mpt90) cc_final: 0.5136 (ttt180)
REVERT: D   70 MET cc_start: 0.8383 (mmt) cc_final: 0.8076 (mmt)
REVERT: D   82 GLU cc_start: 0.7879 (mp0) cc_final: 0.7548 (mp0)
REVERT: D  132 SER cc_start: 0.8885 (m) cc_final: 0.8663 (p)
REVERT: E   72 LEU cc_start: 0.8662 (tp) cc_final: 0.8413 (tt)
REVERT: E   73 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7215 (mt-10)
REVERT: E   74 LEU cc_start: 0.8780 (mp) cc_final: 0.8148 (mt)
REVERT: F   26 GLU cc_start: 0.7483 (pt0) cc_final: 0.6382 (mm-30)
REVERT: F   82 GLU cc_start: 0.6877 (mp0) cc_final: 0.6627 (mp0)
REVERT: F   88 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7220 (tm-30)
REVERT: F  108 GLU cc_start: 0.6558 (mm-30) cc_final: 0.5961 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 286
  average time/residue: 0.1829
  time to fit residues: 72.2212
Evaluate side-chains
  219 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    0.2980
   chunk 33 optimal weight:    0.5980
   chunk 3 optimal weight:    0.2980
   chunk 41 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  23 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.134434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.126296 restraints weight = 15080.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.128580 restraints weight = 8444.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.130136 restraints weight = 5184.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.4715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   7830  Z= 0.227
  Angle     :  0.863  24.948  10626  Z= 0.417
  Chirality :  0.049   0.248   1182
  Planarity :  0.012   0.196   1392
  Dihedral  :  6.313  44.159   1056
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  2.00 %
    Allowed  : 12.45 %
    Favored  : 85.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

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: -1.23 (0.29), residues: 948
  helix:  1.32 (0.37), residues: 198
  sheet:  0.34 (0.30), residues: 303
  loop : -2.80 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  69 
 HIS   0.006   0.001   HIS B   3 
 PHE   0.013   0.002   PHE A 119 
 TYR   0.021   0.002   TYR F 109 
 ARG   0.004   0.000   ARG A   4 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 MET cc_start: 0.7568 (mtp) cc_final: 0.7312 (mtm)
REVERT: A   29 ASN cc_start: 0.7062 (m110) cc_final: 0.6411 (m-40)
REVERT: B    1 MET cc_start: 0.6084 (mpp) cc_final: 0.5695 (mpp)
REVERT: B   17 LYS cc_start: 0.7350 (ptmt) cc_final: 0.6958 (mmmt)
REVERT: B   29 ASN cc_start: 0.7537 (p0) cc_final: 0.7140 (p0)
REVERT: B   40 TYR cc_start: 0.7117 (p90) cc_final: 0.6724 (p90)
REVERT: B   70 MET cc_start: 0.8208 (tpp) cc_final: 0.7922 (mtt)
REVERT: B   88 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7332 (tm-30)
REVERT: B   89 GLN cc_start: 0.7878 (tt0) cc_final: 0.7509 (tt0)
REVERT: B   92 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7442 (mmtm)
REVERT: B   96 ASP cc_start: 0.7356 (m-30) cc_final: 0.7086 (t0)
REVERT: B  101 ILE cc_start: 0.8509 (tt) cc_final: 0.8261 (tt)
REVERT: B  132 SER cc_start: 0.8035 (t) cc_final: 0.7719 (t)
REVERT: C   29 ASN cc_start: 0.7869 (m110) cc_final: 0.7566 (p0)
REVERT: C   70 MET cc_start: 0.8284 (mmm) cc_final: 0.7902 (mmt)
REVERT: C   85 ASP cc_start: 0.6230 (t0) cc_final: 0.5863 (p0)
REVERT: C  141 TYR cc_start: 0.7511 (m-10) cc_final: 0.7254 (m-10)
REVERT: D   46 ARG cc_start: 0.7721 (mpt90) cc_final: 0.5480 (ttt180)
REVERT: D   70 MET cc_start: 0.8439 (mmt) cc_final: 0.8086 (mmt)
REVERT: D   87 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8243 (mm-40)
REVERT: E    1 MET cc_start: 0.7426 (mtp) cc_final: 0.7094 (mtp)
REVERT: E   20 ASP cc_start: 0.7664 (p0) cc_final: 0.6816 (p0)
REVERT: F  108 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5728 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.1690
  time to fit residues: 60.4780
Evaluate side-chains
  210 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 34 optimal weight:    0.0060
   chunk 17 optimal weight:    0.0470
   chunk 60 optimal weight:    0.3980
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 84 optimal weight:    0.2980
   chunk 72 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.2694

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  87 GLN
C  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.137672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.129431 restraints weight = 15098.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.131885 restraints weight = 8172.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.133547 restraints weight = 4889.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.4978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   7830  Z= 0.219
  Angle     :  0.815  19.450  10626  Z= 0.401
  Chirality :  0.048   0.196   1182
  Planarity :  0.011   0.180   1392
  Dihedral  :  6.167  47.783   1056
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  1.79 %
    Allowed  : 12.34 %
    Favored  : 85.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.29), residues: 948
  helix:  1.36 (0.37), residues: 198
  sheet:  0.38 (0.31), residues: 303
  loop : -2.82 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  69 
 HIS   0.005   0.001   HIS B   3 
 PHE   0.012   0.001   PHE B  28 
 TYR   0.018   0.002   TYR B 109 
 ARG   0.003   0.000   ARG F 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 THR cc_start: 0.8537 (p) cc_final: 0.8300 (p)
REVERT: A   29 ASN cc_start: 0.6847 (m110) cc_final: 0.6104 (m-40)
REVERT: B    1 MET cc_start: 0.6136 (mpp) cc_final: 0.5851 (mpp)
REVERT: B   17 LYS cc_start: 0.7437 (ptmt) cc_final: 0.6806 (mmmt)
REVERT: B   40 TYR cc_start: 0.6978 (p90) cc_final: 0.6672 (p90)
REVERT: B   70 MET cc_start: 0.8257 (tpp) cc_final: 0.7887 (mtt)
REVERT: B  132 SER cc_start: 0.8013 (t) cc_final: 0.7796 (t)
REVERT: C   46 ARG cc_start: 0.7030 (ttt180) cc_final: 0.4792 (ttp80)
REVERT: C   70 MET cc_start: 0.8121 (mmm) cc_final: 0.7881 (mmt)
REVERT: C   80 ASP cc_start: 0.7977 (t0) cc_final: 0.7776 (t0)
REVERT: D   28 PHE cc_start: 0.7892 (p90) cc_final: 0.7489 (p90)
REVERT: D   46 ARG cc_start: 0.7529 (mpt90) cc_final: 0.5365 (ttt180)
REVERT: D   70 MET cc_start: 0.8396 (mmt) cc_final: 0.8058 (mmt)
REVERT: D   82 GLU cc_start: 0.7680 (mp0) cc_final: 0.7385 (mp0)
REVERT: D   87 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8195 (mm-40)
REVERT: D   88 GLU cc_start: 0.7715 (tt0) cc_final: 0.7447 (tt0)
REVERT: D   91 GLU cc_start: 0.6513 (pp20) cc_final: 0.6254 (pp20)
REVERT: F  108 GLU cc_start: 0.6055 (mm-30) cc_final: 0.5359 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1687
  time to fit residues: 60.2574
Evaluate side-chains
  205 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 18 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  34 ASN
B  87 GLN
B 115 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.132013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.123761 restraints weight = 15560.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.126119 restraints weight = 8722.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.127645 restraints weight = 5349.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.5176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   7830  Z= 0.246
  Angle     :  0.842  25.862  10626  Z= 0.408
  Chirality :  0.049   0.214   1182
  Planarity :  0.012   0.197   1392
  Dihedral  :  6.185  46.958   1056
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  1.79 %
    Allowed  : 12.55 %
    Favored  : 85.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    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: -1.34 (0.29), residues: 948
  helix:  1.60 (0.38), residues: 198
  sheet: -0.13 (0.29), residues: 327
  loop : -2.88 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  69 
 HIS   0.007   0.002   HIS D   3 
 PHE   0.018   0.002   PHE E 119 
 TYR   0.021   0.002   TYR B 109 
 ARG   0.002   0.000   ARG F 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7038 (m110) cc_final: 0.6369 (m-40)
REVERT: B   17 LYS cc_start: 0.7437 (ptmt) cc_final: 0.7023 (mmmt)
REVERT: B   40 TYR cc_start: 0.7366 (p90) cc_final: 0.7049 (p90)
REVERT: B   70 MET cc_start: 0.8331 (tpp) cc_final: 0.7876 (mtt)
REVERT: B  132 SER cc_start: 0.8172 (t) cc_final: 0.7882 (t)
REVERT: C   46 ARG cc_start: 0.7303 (ttt180) cc_final: 0.5239 (ttp80)
REVERT: C   70 MET cc_start: 0.8117 (mmm) cc_final: 0.7882 (mmt)
REVERT: C   80 ASP cc_start: 0.7933 (t0) cc_final: 0.7545 (t0)
REVERT: C   91 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7067 (tm-30)
REVERT: D   28 PHE cc_start: 0.8174 (p90) cc_final: 0.7689 (p90)
REVERT: D   46 ARG cc_start: 0.7977 (mpt90) cc_final: 0.5859 (ttt180)
REVERT: D   70 MET cc_start: 0.8417 (mmt) cc_final: 0.8052 (mmt)
REVERT: D   91 GLU cc_start: 0.6868 (pp20) cc_final: 0.6609 (pp20)
REVERT: D  132 SER cc_start: 0.8909 (m) cc_final: 0.8633 (p)
REVERT: E    1 MET cc_start: 0.7529 (mtp) cc_final: 0.7294 (mtm)
REVERT: E   20 ASP cc_start: 0.7467 (p0) cc_final: 0.6973 (p0)
REVERT: E   59 THR cc_start: 0.8701 (m) cc_final: 0.8408 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1717
  time to fit residues: 59.9921
Evaluate side-chains
  202 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 68 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0170
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.4024

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  34 ASN
C  38 GLN
** D  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.129142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.121084 restraints weight = 15523.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.123404 restraints weight = 8568.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.124950 restraints weight = 5204.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.5326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   7830  Z= 0.262
  Angle     :  0.852  24.478  10626  Z= 0.418
  Chirality :  0.049   0.194   1182
  Planarity :  0.012   0.191   1392
  Dihedral  :  6.394  50.409   1056
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  1.58 %
    Allowed  : 13.50 %
    Favored  : 84.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    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 (0.29), residues: 948
  helix:  1.41 (0.38), residues: 198
  sheet: -0.16 (0.29), residues: 327
  loop : -2.92 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  69 
 HIS   0.007   0.001   HIS D   3 
 PHE   0.017   0.002   PHE E 119 
 TYR   0.022   0.002   TYR F 109 
 ARG   0.004   0.000   ARG F   4 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7321 (m110) cc_final: 0.6808 (m-40)
REVERT: B   17 LYS cc_start: 0.7413 (ptmt) cc_final: 0.6999 (mmmt)
REVERT: B   40 TYR cc_start: 0.7545 (p90) cc_final: 0.7184 (p90)
REVERT: B   70 MET cc_start: 0.8478 (tpp) cc_final: 0.8089 (mtt)
REVERT: B   87 GLN cc_start: 0.7794 (tt0) cc_final: 0.7356 (tt0)
REVERT: B  132 SER cc_start: 0.8242 (t) cc_final: 0.8027 (t)
REVERT: C   70 MET cc_start: 0.8133 (mmm) cc_final: 0.7907 (mmt)
REVERT: C   80 ASP cc_start: 0.7877 (t0) cc_final: 0.7397 (t0)
REVERT: D   28 PHE cc_start: 0.8107 (p90) cc_final: 0.7608 (p90)
REVERT: D   46 ARG cc_start: 0.8108 (mpt90) cc_final: 0.5972 (ttt180)
REVERT: D   70 MET cc_start: 0.8430 (mmt) cc_final: 0.8050 (mmt)
REVERT: D   82 GLU cc_start: 0.7720 (mp0) cc_final: 0.7409 (mp0)
REVERT: D   87 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8284 (mm-40)
REVERT: D  132 SER cc_start: 0.8973 (m) cc_final: 0.8710 (p)
REVERT: E   85 ASP cc_start: 0.7111 (t0) cc_final: 0.6906 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.1599
  time to fit residues: 54.7454
Evaluate side-chains
  186 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  87 GLN
C  38 GLN
D  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.124128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.116400 restraints weight = 15606.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.118620 restraints weight = 8549.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.120134 restraints weight = 5186.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.5525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   7830  Z= 0.305
  Angle     :  0.885  22.673  10626  Z= 0.437
  Chirality :  0.050   0.195   1182
  Planarity :  0.012   0.186   1392
  Dihedral  :  6.642  49.646   1056
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  1.58 %
    Allowed  : 13.61 %
    Favored  : 84.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    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: -1.62 (0.28), residues: 948
  helix:  1.35 (0.38), residues: 198
  sheet: -0.33 (0.29), residues: 327
  loop : -3.00 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  69 
 HIS   0.010   0.002   HIS D   3 
 PHE   0.016   0.002   PHE E 119 
 TYR   0.026   0.002   TYR D 109 
 ARG   0.006   0.001   ARG F   4 

===============================================================================
Job complete
usr+sys time: 2450.42 seconds
wall clock time: 45 minutes 4.82 seconds (2704.82 seconds total)