Starting phenix.real_space_refine
on Wed Sep 17 16:53:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gmd_51448/09_2025/9gmd_51448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gmd_51448/09_2025/9gmd_51448.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/9gmd_51448/09_2025/9gmd_51448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gmd_51448/09_2025/9gmd_51448.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gmd_51448/09_2025/9gmd_51448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gmd_51448/09_2025/9gmd_51448.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3144      2.51       5
     N     882      2.21       5
     O     948      1.98       5
     H    4925      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9919
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1224
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 557
          Classifications: {'peptide': 38}
          Link IDs: {'TRANS': 37}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 3333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 3333
          Classifications: {'peptide': 205}
          Link IDs: {'PTRANS': 9, 'TRANS': 195}
    Chain: "F"
      Number of atoms: 3305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 3305
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 8, 'TRANS': 194}
    Chain: "I"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 738
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "J"
      Number of atoms: 762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 762
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
  Time building chain proxies: 1.80, per 1000 atoms: 0.18
  Number of scatterers: 9919
  At special positions: 0
  Unit cell: (83.953, 91.0677, 92.4906, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     O     948      8.00
     N     882      7.00
     C    3144      6.00
     H    4925      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 219.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1162

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      68.1% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'C' and resid 191 through 196
      removed outlier: 3.620A  pdb=" N   ASP C 196 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 289
      removed outlier: 3.657A  pdb=" N   GLN C 268 " --> pdb=" O   ILE C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 307
      removed outlier: 3.669A  pdb=" N   GLN C 299 " --> pdb=" O   ARG C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 311
    Processing helix  chain 'D' and resid 48 through 55
    Processing helix  chain 'D' and resid 70 through 79
    Processing helix  chain 'D' and resid 95 through 99
      removed outlier: 4.298A  pdb=" N   ALA D  99 " --> pdb=" O   GLU D  96 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 11 through 19
    Processing helix  chain 'E' and resid 22 through 31
      removed outlier: 3.825A  pdb=" N   LEU E  26 " --> pdb=" O   LEU E  22 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG E  31 " --> pdb=" O   ASP E  27 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 50
    Processing helix  chain 'E' and resid 50 through 59
    Processing helix  chain 'E' and resid 89 through 105
      removed outlier: 3.739A  pdb=" N   LEU E 104 " --> pdb=" O   CYS E 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 112
      removed outlier: 3.649A  pdb=" N   LEU E 109 " --> pdb=" O   PRO E 106 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA E 110 " --> pdb=" O   GLU E 107 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 117 through 125
    Processing helix  chain 'E' and resid 129 through 138
      removed outlier: 4.170A  pdb=" N   LEU E 136 " --> pdb=" O   LYS E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 165
      removed outlier: 3.597A  pdb=" N   ARG E 156 " --> pdb=" O   GLN E 152 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU E 165 " --> pdb=" O   ARG E 161 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 187
    Processing helix  chain 'E' and resid 188 through 193
      removed outlier: 4.620A  pdb=" N   ALA E 193 " --> pdb=" O   ALA E 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 208
    Processing helix  chain 'F' and resid 11 through 19
    Processing helix  chain 'F' and resid 22 through 32
      removed outlier: 3.677A  pdb=" N   LEU F  26 " --> pdb=" O   LEU F  22 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 50
    Processing helix  chain 'F' and resid 50 through 59
      removed outlier: 3.597A  pdb=" N   LEU F  54 " --> pdb=" O   PHE F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 89 through 104
      removed outlier: 3.819A  pdb=" N   LEU F 104 " --> pdb=" O   CYS F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 106 through 112
      removed outlier: 4.267A  pdb=" N   ALA F 110 " --> pdb=" O   PRO F 106 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 116 through 128
      removed outlier: 3.586A  pdb=" N   LEU F 120 " --> pdb=" O   THR F 116 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 138
    Processing helix  chain 'F' and resid 144 through 166
      removed outlier: 3.576A  pdb=" N   ARG F 148 " --> pdb=" O   SER F 144 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 182 through 192
      removed outlier: 3.580A  pdb=" N   PHE F 185 " --> pdb=" O   GLU F 182 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ALA F 189 " --> pdb=" O   ARG F 186 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   ASP F 190 " --> pdb=" O   PHE F 187 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 208
    Processing helix  chain 'I' and resid 10 through 49
      removed outlier: 3.538A  pdb=" N   ASN I  32 " --> pdb=" O   ASP I  28 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 10 through 49
      removed outlier: 4.285A  pdb=" N   ASP J  15 " --> pdb=" O   ASP J  11 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ILE J  16 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLN J  17 " --> pdb=" O   TRP J  13 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP J  21 " --> pdb=" O   GLN J  17 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 313 through 315
      removed outlier: 3.747A  pdb=" N   ALA C 314 " --> pdb=" O   MET E 211 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 317 through 318
    Processing sheet with id=AA3, first strand: chain 'C' and resid 323 through 325
      removed outlier: 5.828A  pdb=" N   LEU C 323 " --> pdb=" O   SER F  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 63 through 66
    Processing sheet with id=AA5, first strand: chain 'E' and resid 114 through 116
      removed outlier: 3.743A  pdb=" N   PHE E 178 " --> pdb=" O   PHE E 115 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 63 through 67
    Processing sheet with id=AA7, first strand: chain 'F' and resid 114 through 115
    Processing sheet with id=AA8, first strand: chain 'I' and resid 5 through 9

    288 hydrogen bonds defined for protein.
    819 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4923
        1.03 -     1.23: 4
        1.23 -     1.42: 2155
        1.42 -     1.61: 2882
        1.61 -     1.81: 38
  Bond restraints: 10002
  Sorted by residual:
  bond pdb=" CB  PRO E 197 "
       pdb=" CG  PRO E 197 "
    ideal  model  delta    sigma   weight residual
    1.492  1.612 -0.120 5.00e-02 4.00e+02 5.79e+00
  bond pdb=" CG  LEU E 127 "
       pdb=" CD2 LEU E 127 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.44e+00
  bond pdb=" CB  LYS C 283 "
       pdb=" CG  LYS C 283 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CB  GLU I  24 "
       pdb=" CG  GLU I  24 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" CG  LYS E 132 "
       pdb=" CD  LYS E 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.44e-01
  ... (remaining 9997 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 17805
        1.79 -     3.58: 180
        3.58 -     5.37: 24
        5.37 -     7.16: 1
        7.16 -     8.94: 1
  Bond angle restraints: 18011
  Sorted by residual:
  angle pdb=" CA  PRO E 197 "
        pdb=" N   PRO E 197 "
        pdb=" CD  PRO E 197 "
      ideal   model   delta    sigma   weight residual
     112.00  103.06    8.94 1.40e+00 5.10e-01 4.08e+01
  angle pdb=" N   ASP C 292 "
        pdb=" CA  ASP C 292 "
        pdb=" C   ASP C 292 "
      ideal   model   delta    sigma   weight residual
     110.44  107.15    3.29 1.20e+00 6.94e-01 7.51e+00
  angle pdb=" N   PRO E 197 "
        pdb=" CA  PRO E 197 "
        pdb=" CB  PRO E 197 "
      ideal   model   delta    sigma   weight residual
     103.25  100.44    2.81 1.05e+00 9.07e-01 7.18e+00
  angle pdb=" CA  LYS C 283 "
        pdb=" CB  LYS C 283 "
        pdb=" CG  LYS C 283 "
      ideal   model   delta    sigma   weight residual
     114.10  119.10   -5.00 2.00e+00 2.50e-01 6.25e+00
  angle pdb=" CA  GLU I  24 "
        pdb=" CB  GLU I  24 "
        pdb=" CG  GLU I  24 "
      ideal   model   delta    sigma   weight residual
     114.10  119.00   -4.90 2.00e+00 2.50e-01 6.01e+00
  ... (remaining 18006 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.88: 4065
       16.88 -    33.76: 402
       33.76 -    50.63: 135
       50.63 -    67.51: 44
       67.51 -    84.39: 7
  Dihedral angle restraints: 4653
    sinusoidal: 2577
      harmonic: 2076
  Sorted by residual:
  dihedral pdb=" CG  ARG F 108 "
           pdb=" CD  ARG F 108 "
           pdb=" NE  ARG F 108 "
           pdb=" CZ  ARG F 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.67   43.67     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG E  60 "
           pdb=" CD  ARG E  60 "
           pdb=" NE  ARG E  60 "
           pdb=" CZ  ARG E  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.91  -43.09     2      1.50e+01 4.44e-03 9.96e+00
  dihedral pdb=" CB  GLU E 119 "
           pdb=" CG  GLU E 119 "
           pdb=" CD  GLU E 119 "
           pdb=" OE1 GLU E 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.39   84.39     1      3.00e+01 1.11e-03 9.62e+00
  ... (remaining 4650 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 495
       0.027 -    0.053: 161
       0.053 -    0.080: 51
       0.080 -    0.106: 27
       0.106 -    0.133: 10
  Chirality restraints: 744
  Sorted by residual:
  chirality pdb=" CA  ILE J   8 "
            pdb=" N   ILE J   8 "
            pdb=" C   ILE J   8 "
            pdb=" CB  ILE J   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  PRO E 197 "
            pdb=" N   PRO E 197 "
            pdb=" C   PRO E 197 "
            pdb=" CB  PRO E 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CA  ILE F  83 "
            pdb=" N   ILE F  83 "
            pdb=" C   ILE F  83 "
            pdb=" CB  ILE F  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.70e-01
  ... (remaining 741 not shown)

  Planarity restraints: 1483
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 196 "   -0.077 5.00e-02 4.00e+02   1.11e-01 1.99e+01
        pdb=" N   PRO E 197 "    0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO E 197 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO E 197 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 302 "   -0.358 9.50e-02 1.11e+02   1.20e-01 1.58e+01
        pdb=" NE  ARG C 302 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 302 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 302 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 302 "   -0.006 2.00e-02 2.50e+03
        pdb="HH11 ARG C 302 "   -0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG C 302 "    0.003 2.00e-02 2.50e+03
        pdb="HH21 ARG C 302 "   -0.004 2.00e-02 2.50e+03
        pdb="HH22 ARG C 302 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 286 "   -0.151 9.50e-02 1.11e+02   5.05e-02 3.10e+00
        pdb=" NE  ARG C 286 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 286 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 286 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 286 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG C 286 "    0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG C 286 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG C 286 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG C 286 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1480 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 386
        2.15 -     2.77: 18806
        2.77 -     3.38: 27108
        3.38 -     3.99: 31872
        3.99 -     4.60: 50047
  Nonbonded interactions: 128219
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU F 119 "
            pdb=" H   GLU F 119 "
     model   vdw
     1.542 2.450
  nonbonded pdb="HH12 ARG C 300 "
            pdb=" O   ALA E 193 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" OE1 GLU E  52 "
            pdb=" H   GLU E  52 "
     model   vdw
     1.586 2.450
  nonbonded pdb=" OE1 GLU F  40 "
            pdb=" H   GLU F  40 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" HG  SER E 175 "
            pdb=" OG  SER I  22 "
     model   vdw
     1.645 2.450
  ... (remaining 128214 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 'E' and resid 9 through 209)
  selection = (chain 'F' and resid 9 through 209)
}
ncs_group {
  reference = chain 'I'
  selection = (chain 'J' and resid 4 through 49)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:             0.060
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.760
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
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      :  0.004   0.120   5077  Z= 0.175
  Angle     :  0.615   8.944   6843  Z= 0.336
  Chirality :  0.035   0.133    744
  Planarity :  0.008   0.159    901
  Dihedral  : 16.616  84.391   1941
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 22.30 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.35), residues: 593
  helix:  1.89 (0.27), residues: 371
  sheet:  0.92 (1.07), residues: 22
  loop : -0.32 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 286 
 TYR   0.015   0.002   TYR E 101 
 PHE   0.008   0.001   PHE F  73 
 TRP   0.025   0.002   TRP I  13 
 HIS   0.005   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 5077)
  covalent geometry    : angle       0.61464 ( 6843)
  hydrogen bonds       : bond        0.16852 (  288)
  hydrogen bonds       : angle       5.83350 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8214 (m-70) cc_final: 0.7794 (m-70)
REVERT: I   27 ASN cc_start: 0.8791 (t0) cc_final: 0.8291 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2586
  time to fit residues: 46.1630
Evaluate side-chains
  127 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.9242

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

Flipped N/Q/H residues before XYZ refinement:
I  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.088264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.064299 restraints weight = 43198.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.067899 restraints weight = 19323.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.070128 restraints weight = 11777.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.071506 restraints weight = 8733.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.072338 restraints weight = 7311.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5077  Z= 0.156
  Angle     :  0.575   5.653   6843  Z= 0.308
  Chirality :  0.035   0.146    744
  Planarity :  0.005   0.059    901
  Dihedral  :  3.850  16.344    681
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.49 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.35), residues: 593
  helix:  1.85 (0.27), residues: 389
  sheet:  1.13 (1.08), residues: 22
  loop : -0.53 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 300 
 TYR   0.013   0.002   TYR E 101 
 PHE   0.009   0.001   PHE C 297 
 TRP   0.007   0.001   TRP I  13 
 HIS   0.004   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 5077)
  covalent geometry    : angle       0.57463 ( 6843)
  hydrogen bonds       : bond        0.04595 (  288)
  hydrogen bonds       : angle       4.71854 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  268 GLN cc_start: 0.9030 (mp10) cc_final: 0.8776 (mp10)
REVERT: C  282 HIS cc_start: 0.8853 (m-70) cc_final: 0.8218 (m-70)
REVERT: C  311 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8412 (tm-30)
REVERT: E   93 MET cc_start: 0.9079 (mmm) cc_final: 0.8838 (mmm)
REVERT: E  167 MET cc_start: 0.9365 (mmp) cc_final: 0.9163 (mmp)
REVERT: F   10 MET cc_start: 0.8126 (ppp) cc_final: 0.7887 (ppp)
REVERT: I   14 ASN cc_start: 0.9019 (m-40) cc_final: 0.8623 (m110)
REVERT: I   24 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: I   28 ASP cc_start: 0.9060 (m-30) cc_final: 0.8796 (m-30)
REVERT: J    8 ILE cc_start: 0.9060 (mt) cc_final: 0.8766 (tt)
REVERT: J   19 TYR cc_start: 0.8402 (t80) cc_final: 0.8054 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 136
  average time/residue: 0.1885
  time to fit residues: 31.1117
Evaluate side-chains
  128 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.088171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.064177 restraints weight = 43122.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.067778 restraints weight = 19135.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.070030 restraints weight = 11692.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.071424 restraints weight = 8663.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.072143 restraints weight = 7238.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5077  Z= 0.130
  Angle     :  0.531   6.062   6843  Z= 0.282
  Chirality :  0.034   0.133    744
  Planarity :  0.004   0.050    901
  Dihedral  :  3.774  15.801    681
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.12 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.36), residues: 593
  helix:  2.10 (0.27), residues: 389
  sheet:  1.00 (1.07), residues: 22
  loop : -0.51 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 286 
 TYR   0.013   0.001   TYR E 101 
 PHE   0.016   0.001   PHE F 115 
 TRP   0.009   0.001   TRP C 266 
 HIS   0.003   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5077)
  covalent geometry    : angle       0.53099 ( 6843)
  hydrogen bonds       : bond        0.04028 (  288)
  hydrogen bonds       : angle       4.36920 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8823 (m-70) cc_final: 0.8194 (m-70)
REVERT: C  311 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8330 (tm-30)
REVERT: E  167 MET cc_start: 0.9361 (mmp) cc_final: 0.8928 (mmp)
REVERT: E  182 GLU cc_start: 0.8870 (pm20) cc_final: 0.8558 (pm20)
REVERT: I   14 ASN cc_start: 0.9021 (m-40) cc_final: 0.8597 (m110)
REVERT: I   24 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8476 (tm-30)
REVERT: I   28 ASP cc_start: 0.9232 (m-30) cc_final: 0.8871 (m-30)
REVERT: J    8 ILE cc_start: 0.9004 (mt) cc_final: 0.8787 (tt)
REVERT: J   19 TYR cc_start: 0.8414 (t80) cc_final: 0.7943 (t80)
REVERT: J   23 LEU cc_start: 0.9133 (mp) cc_final: 0.8846 (mp)
  outliers start: 12
  outliers final: 9
  residues processed: 130
  average time/residue: 0.2204
  time to fit residues: 34.3996
Evaluate side-chains
  130 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue  177 LYS
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.084541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.061115 restraints weight = 43950.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.064532 restraints weight = 19454.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.066665 restraints weight = 11882.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.067956 restraints weight = 8833.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.068749 restraints weight = 7422.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5077  Z= 0.256
  Angle     :  0.597   6.599   6843  Z= 0.328
  Chirality :  0.036   0.159    744
  Planarity :  0.004   0.048    901
  Dihedral  :  4.066  18.397    681
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.98 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.34), residues: 593
  helix:  1.65 (0.26), residues: 387
  sheet:  0.64 (1.08), residues: 22
  loop : -0.94 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 163 
 TYR   0.013   0.002   TYR C 277 
 PHE   0.013   0.002   PHE F 115 
 TRP   0.009   0.001   TRP E 169 
 HIS   0.006   0.002   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 5077)
  covalent geometry    : angle       0.59703 ( 6843)
  hydrogen bonds       : bond        0.04324 (  288)
  hydrogen bonds       : angle       4.80322 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  278 ASP cc_start: 0.9023 (t70) cc_final: 0.8704 (t70)
REVERT: C  282 HIS cc_start: 0.8801 (m-70) cc_final: 0.8159 (m-70)
REVERT: E  182 GLU cc_start: 0.8896 (pm20) cc_final: 0.8681 (pm20)
REVERT: I   24 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8667 (tm-30)
REVERT: I   28 ASP cc_start: 0.9313 (m-30) cc_final: 0.9046 (m-30)
REVERT: J    8 ILE cc_start: 0.9145 (mt) cc_final: 0.8902 (tt)
REVERT: J   19 TYR cc_start: 0.8434 (t80) cc_final: 0.8185 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2289
  time to fit residues: 35.1953
Evaluate side-chains
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.086710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.063007 restraints weight = 42913.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.066508 restraints weight = 19058.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.068696 restraints weight = 11655.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.070000 restraints weight = 8663.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.070818 restraints weight = 7282.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5077  Z= 0.131
  Angle     :  0.520   6.690   6843  Z= 0.274
  Chirality :  0.034   0.132    744
  Planarity :  0.004   0.050    901
  Dihedral  :  3.846  16.725    681
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 24.54 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.35), residues: 593
  helix:  2.02 (0.27), residues: 389
  sheet:  0.68 (1.06), residues: 22
  loop : -0.74 (0.46), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  25 
 TYR   0.011   0.001   TYR C 277 
 PHE   0.005   0.001   PHE C 297 
 TRP   0.013   0.001   TRP C 266 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5077)
  covalent geometry    : angle       0.52047 ( 6843)
  hydrogen bonds       : bond        0.03709 (  288)
  hydrogen bonds       : angle       4.32804 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8708 (m-70) cc_final: 0.8107 (m-70)
REVERT: E   39 ASP cc_start: 0.7969 (t0) cc_final: 0.7576 (t0)
REVERT: I   14 ASN cc_start: 0.9040 (m-40) cc_final: 0.8429 (m110)
REVERT: I   24 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8429 (tm-30)
REVERT: I   28 ASP cc_start: 0.9274 (m-30) cc_final: 0.8803 (m-30)
REVERT: J   19 TYR cc_start: 0.8378 (t80) cc_final: 0.8151 (t80)
REVERT: J   24 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7248 (mt-10)
  outliers start: 13
  outliers final: 10
  residues processed: 131
  average time/residue: 0.2400
  time to fit residues: 37.5339
Evaluate side-chains
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue  151 LEU
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 149 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.084177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.061100 restraints weight = 44115.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.064407 restraints weight = 19914.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.066448 restraints weight = 12289.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.067644 restraints weight = 9189.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.068438 restraints weight = 7776.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5077  Z= 0.232
  Angle     :  0.584   7.326   6843  Z= 0.316
  Chirality :  0.035   0.137    744
  Planarity :  0.004   0.048    901
  Dihedral  :  3.984  17.465    681
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 25.46 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.35), residues: 593
  helix:  1.75 (0.27), residues: 388
  sheet:  0.53 (1.09), residues: 22
  loop : -0.91 (0.46), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  25 
 TYR   0.013   0.002   TYR C 277 
 PHE   0.012   0.001   PHE F  57 
 TRP   0.019   0.002   TRP C 266 
 HIS   0.005   0.001   HIS C 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 5077)
  covalent geometry    : angle       0.58407 ( 6843)
  hydrogen bonds       : bond        0.04000 (  288)
  hydrogen bonds       : angle       4.69064 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8762 (m-70) cc_final: 0.8194 (m-70)
REVERT: F  170 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.5751 (p90)
REVERT: I   24 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8628 (tm-30)
REVERT: I   28 ASP cc_start: 0.9299 (m-30) cc_final: 0.8995 (m-30)
REVERT: J   19 TYR cc_start: 0.8259 (t80) cc_final: 0.8038 (t80)
  outliers start: 17
  outliers final: 14
  residues processed: 127
  average time/residue: 0.2170
  time to fit residues: 33.1580
Evaluate side-chains
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain F residue  151 LEU
Chi-restraints excluded: chain F residue  170 PHE
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0170
   chunk 54 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.2022

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.084958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.062049 restraints weight = 43425.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.065342 restraints weight = 19452.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.067392 restraints weight = 11976.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.068668 restraints weight = 8944.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.069357 restraints weight = 7511.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5077  Z= 0.179
  Angle     :  0.562   7.361   6843  Z= 0.297
  Chirality :  0.035   0.129    744
  Planarity :  0.004   0.048    901
  Dihedral  :  3.918  17.671    681
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.46 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.36), residues: 593
  helix:  1.89 (0.27), residues: 390
  sheet:  0.41 (1.09), residues: 22
  loop : -0.81 (0.47), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  25 
 TYR   0.012   0.002   TYR E 101 
 PHE   0.007   0.001   PHE F  57 
 TRP   0.023   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 5077)
  covalent geometry    : angle       0.56170 ( 6843)
  hydrogen bonds       : bond        0.03721 (  288)
  hydrogen bonds       : angle       4.50813 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8745 (m-70) cc_final: 0.8208 (m-70)
REVERT: E   39 ASP cc_start: 0.8017 (t0) cc_final: 0.7637 (t0)
REVERT: E  211 MET cc_start: 0.7566 (ptt) cc_final: 0.7335 (ptt)
REVERT: F  150 LYS cc_start: 0.9569 (mttt) cc_final: 0.9247 (ptpp)
REVERT: I   14 ASN cc_start: 0.9072 (m-40) cc_final: 0.8622 (m110)
REVERT: I   24 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8604 (tm-30)
REVERT: I   28 ASP cc_start: 0.9277 (m-30) cc_final: 0.8962 (m-30)
  outliers start: 14
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2254
  time to fit residues: 34.6978
Evaluate side-chains
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain F residue  133 LEU
Chi-restraints excluded: chain F residue  151 LEU
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN
C 303 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.085965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.062976 restraints weight = 42798.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.066392 restraints weight = 18701.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068494 restraints weight = 11318.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.069789 restraints weight = 8354.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.070507 restraints weight = 6991.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5077  Z= 0.135
  Angle     :  0.545   7.570   6843  Z= 0.283
  Chirality :  0.034   0.132    744
  Planarity :  0.004   0.048    901
  Dihedral  :  3.792  16.829    681
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 26.21 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.36), residues: 593
  helix:  2.22 (0.27), residues: 384
  sheet:  0.47 (1.08), residues: 22
  loop : -0.60 (0.47), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  25 
 TYR   0.010   0.001   TYR C 277 
 PHE   0.005   0.001   PHE F  57 
 TRP   0.027   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5077)
  covalent geometry    : angle       0.54464 ( 6843)
  hydrogen bonds       : bond        0.03464 (  288)
  hydrogen bonds       : angle       4.29563 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8768 (m-70) cc_final: 0.8249 (m-70)
REVERT: E   39 ASP cc_start: 0.8038 (t0) cc_final: 0.7656 (t0)
REVERT: E  211 MET cc_start: 0.7615 (ptt) cc_final: 0.7398 (ptt)
REVERT: I   14 ASN cc_start: 0.9031 (m-40) cc_final: 0.8554 (m110)
REVERT: I   24 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8580 (tm-30)
REVERT: I   28 ASP cc_start: 0.9252 (m-30) cc_final: 0.8932 (m-30)
  outliers start: 14
  outliers final: 13
  residues processed: 134
  average time/residue: 0.2165
  time to fit residues: 34.8610
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain F residue  133 LEU
Chi-restraints excluded: chain F residue  151 LEU
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.085776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.062646 restraints weight = 43271.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.066093 restraints weight = 18938.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.068211 restraints weight = 11473.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.069509 restraints weight = 8482.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.070218 restraints weight = 7106.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5077  Z= 0.143
  Angle     :  0.553   7.944   6843  Z= 0.289
  Chirality :  0.034   0.145    744
  Planarity :  0.004   0.049    901
  Dihedral  :  3.784  16.590    681
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.84 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.36), residues: 593
  helix:  2.29 (0.27), residues: 384
  sheet:  0.13 (1.05), residues: 22
  loop : -0.57 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  25 
 TYR   0.020   0.001   TYR D 101 
 PHE   0.006   0.001   PHE F  57 
 TRP   0.033   0.001   TRP C 266 
 HIS   0.004   0.001   HIS C 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5077)
  covalent geometry    : angle       0.55254 ( 6843)
  hydrogen bonds       : bond        0.03385 (  288)
  hydrogen bonds       : angle       4.25589 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8771 (m-70) cc_final: 0.8244 (m-70)
REVERT: C  302 ARG cc_start: 0.8712 (ttm170) cc_final: 0.8247 (tpp80)
REVERT: E   39 ASP cc_start: 0.8012 (t0) cc_final: 0.7629 (t0)
REVERT: E  211 MET cc_start: 0.7591 (ptt) cc_final: 0.7354 (ptt)
REVERT: I   14 ASN cc_start: 0.9016 (m-40) cc_final: 0.8423 (m110)
REVERT: I   24 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: I   28 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8936 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2354
  time to fit residues: 36.2239
Evaluate side-chains
  129 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain I residue    7 THR
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   28 ASP
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0980
   chunk 23 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0970
   chunk 39 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0050
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.2192

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN
E 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.088902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.065321 restraints weight = 43761.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.068926 restraints weight = 19550.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.071191 restraints weight = 11993.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.072564 restraints weight = 8906.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.073256 restraints weight = 7459.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5077  Z= 0.106
  Angle     :  0.545   7.993   6843  Z= 0.279
  Chirality :  0.034   0.127    744
  Planarity :  0.004   0.052    901
  Dihedral  :  3.612  16.965    681
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 26.02 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.40 (0.36), residues: 593
  helix:  2.61 (0.27), residues: 384
  sheet:  0.21 (1.05), residues: 22
  loop : -0.43 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  25 
 TYR   0.008   0.001   TYR C 277 
 PHE   0.005   0.001   PHE F 185 
 TRP   0.036   0.002   TRP C 266 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 5077)
  covalent geometry    : angle       0.54480 ( 6843)
  hydrogen bonds       : bond        0.03056 (  288)
  hydrogen bonds       : angle       3.97304 (  819)

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

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

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1186 Ramachandran restraints generated.
    593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  282 HIS cc_start: 0.8736 (m-70) cc_final: 0.8205 (m-70)
REVERT: C  286 ARG cc_start: 0.8748 (ttp80) cc_final: 0.8424 (ttm-80)
REVERT: C  302 ARG cc_start: 0.8604 (ttm170) cc_final: 0.8176 (tpp80)
REVERT: E   39 ASP cc_start: 0.7749 (t0) cc_final: 0.7371 (t0)
REVERT: E   94 MET cc_start: 0.9100 (mtp) cc_final: 0.8837 (mtt)
REVERT: E  167 MET cc_start: 0.9309 (mmp) cc_final: 0.9104 (mmp)
REVERT: E  211 MET cc_start: 0.7479 (ptt) cc_final: 0.7241 (ptt)
REVERT: I   14 ASN cc_start: 0.8906 (m-40) cc_final: 0.8454 (m110)
REVERT: I   24 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8386 (tm-30)
REVERT: I   28 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8753 (m-30)
REVERT: I   40 TYR cc_start: 0.8952 (t80) cc_final: 0.8717 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 131
  average time/residue: 0.2243
  time to fit residues: 35.1982
Evaluate side-chains
  132 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain F residue   44 HIS
Chi-restraints excluded: chain F residue  100 CYS
Chi-restraints excluded: chain I residue   27 ASN
Chi-restraints excluded: chain I residue   28 ASP
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain J residue   31 LYS
Chi-restraints excluded: chain J residue   44 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0270
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0770
   chunk 18 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
C 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.088155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.064985 restraints weight = 44325.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.068429 restraints weight = 19929.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.070653 restraints weight = 12353.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.071998 restraints weight = 9186.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.072783 restraints weight = 7716.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5077  Z= 0.118
  Angle     :  0.544   8.128   6843  Z= 0.281
  Chirality :  0.034   0.130    744
  Planarity :  0.004   0.048    901
  Dihedral  :  3.593  16.272    681
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 25.84 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.36), residues: 593
  helix:  2.66 (0.27), residues: 384
  sheet:  0.15 (1.05), residues: 22
  loop : -0.45 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  25 
 TYR   0.012   0.001   TYR C 308 
 PHE   0.005   0.001   PHE F  72 
 TRP   0.035   0.002   TRP C 266 
 HIS   0.003   0.001   HIS C 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5077)
  covalent geometry    : angle       0.54419 ( 6843)
  hydrogen bonds       : bond        0.03187 (  288)
  hydrogen bonds       : angle       4.06973 (  819)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2104.10 seconds
wall clock time: 36 minutes 23.55 seconds (2183.55 seconds total)