Starting phenix.real_space_refine
on Tue Feb  3 20:50:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fl9_50536/02_2026/9fl9_50536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fl9_50536/02_2026/9fl9_50536.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fl9_50536/02_2026/9fl9_50536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fl9_50536/02_2026/9fl9_50536.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fl9_50536/02_2026/9fl9_50536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fl9_50536/02_2026/9fl9_50536.map"
  }
  resolution = 3.74
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4270      2.51       5
     N    1196      2.21       5
     O    1264      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6769
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1370
          Classifications: {'peptide': 174}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 168}
    Chain: "B"
      Number of atoms: 1820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1820
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220}
    Chain: "C"
      Number of atoms: 2540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2540
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 320}
    Chain: "D"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 663
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 76}
    Chain: "E"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 376
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
  Time building chain proxies: 1.74, per 1000 atoms: 0.26
  Number of scatterers: 6769
  At special positions: 0
  Unit cell: (65.45, 78.54, 150.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1264      8.00
     N    1196      7.00
     C    4270      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 284.2 milliseconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1610

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      47.6% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 35
      removed outlier: 3.810A  pdb=" N   ARG A  30 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 66
      removed outlier: 4.268A  pdb=" N   ILE A  54 " --> pdb=" O   ASP A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 84
      removed outlier: 3.785A  pdb=" N   ILE A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   PHE A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   SER A  84 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 118 through 126
      removed outlier: 3.515A  pdb=" N   LEU A 122 " --> pdb=" O   ASN A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 140
      removed outlier: 3.527A  pdb=" N   ILE A 139 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 146
      removed outlier: 3.547A  pdb=" N   LYS A 146 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 160 through 167
      removed outlier: 3.683A  pdb=" N   ALA A 164 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 33
    Processing helix  chain 'B' and resid 72 through 95
    Processing helix  chain 'B' and resid 121 through 129
    Processing helix  chain 'B' and resid 130 through 132
      No H-bonds generated for 'chain 'B' and resid 130 through 132'
    Processing helix  chain 'B' and resid 137 through 154
    Processing helix  chain 'B' and resid 164 through 166
      No H-bonds generated for 'chain 'B' and resid 164 through 166'
    Processing helix  chain 'B' and resid 192 through 211
    Processing helix  chain 'B' and resid 214 through 229
    Processing helix  chain 'B' and resid 231 through 244
      removed outlier: 4.064A  pdb=" N   VAL B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 65
      removed outlier: 4.355A  pdb=" N   LEU C  54 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   ASP C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 101
      removed outlier: 4.334A  pdb=" N   VAL C  92 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA C  93 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 122
    Processing helix  chain 'C' and resid 156 through 168
    Processing helix  chain 'C' and resid 175 through 183
    Processing helix  chain 'C' and resid 204 through 221
      removed outlier: 3.725A  pdb=" N   PHE C 210 " --> pdb=" O   GLY C 206 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA C 215 " --> pdb=" O   ILE C 211 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   HIS C 216 " --> pdb=" O   GLU C 212 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ARG C 217 " --> pdb=" O   ASP C 213 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR C 221 " --> pdb=" O   ARG C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 253
      removed outlier: 3.811A  pdb=" N   LEU C 229 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 280
    Processing helix  chain 'C' and resid 296 through 309
      removed outlier: 3.516A  pdb=" N   GLU C 305 " --> pdb=" O   GLN C 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 81
      removed outlier: 3.538A  pdb=" N   ALA D  75 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 137
    Processing helix  chain 'E' and resid 29 through 49
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 21
    Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 42
    Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171
      removed outlier: 4.363A  pdb=" N   ASN B 178 " --> pdb=" O   LYS B 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 26
      removed outlier: 5.599A  pdb=" N   VAL C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   ARG C  20 " --> pdb=" O   VAL C  24 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA C  26 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   ALA C  75 " --> pdb=" O   ALA C   3 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   LEU C   5 " --> pdb=" O   ALA C  75 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   THR C  77 " --> pdb=" O   LEU C   5 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL C 105 " --> pdb=" O   ILE C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 145 through 151
      removed outlier: 5.884A  pdb=" N   VAL C 138 " --> pdb=" O   PHE C 149 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLU C 151 " --> pdb=" O   THR C 136 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   THR C 136 " --> pdb=" O   GLU C 151 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASN C 135 " --> pdb=" O   SER C 132 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL C 260 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 94 through 100
      removed outlier: 6.012A  pdb=" N   GLU E   2 " --> pdb=" O   PRO D  68 " (cutoff:3.500A)

    350 hydrogen bonds defined for protein.
    1014 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: 0.99

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2270
        1.34 -     1.46: 1027
        1.46 -     1.57: 3523
        1.57 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 6883
  Sorted by residual:
  bond pdb=" C   ARG C  29 "
       pdb=" N   ARG C  30 "
    ideal  model  delta    sigma   weight residual
    1.336  1.316  0.020 1.87e-02 2.86e+03 1.15e+00
  bond pdb=" N   ASP B 162 "
       pdb=" CA  ASP B 162 "
    ideal  model  delta    sigma   weight residual
    1.465  1.451  0.014 1.31e-02 5.83e+03 1.14e+00
  bond pdb=" CA  GLY C 106 "
       pdb=" C   GLY C 106 "
    ideal  model  delta    sigma   weight residual
    1.520  1.510  0.011 9.90e-03 1.02e+04 1.13e+00
  bond pdb=" C   VAL D  92 "
       pdb=" O   VAL D  92 "
    ideal  model  delta    sigma   weight residual
    1.236  1.224  0.012 1.19e-02 7.06e+03 1.06e+00
  bond pdb=" CB  GLU D  74 "
       pdb=" CG  GLU D  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 1.02e+00
  ... (remaining 6878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 8861
        1.66 -     3.32: 354
        3.32 -     4.98: 64
        4.98 -     6.64: 21
        6.64 -     8.30: 3
  Bond angle restraints: 9303
  Sorted by residual:
  angle pdb=" N   ILE C 153 "
        pdb=" CA  ILE C 153 "
        pdb=" C   ILE C 153 "
      ideal   model   delta    sigma   weight residual
     113.71  109.31    4.40 9.50e-01 1.11e+00 2.15e+01
  angle pdb=" N   LYS A 134 "
        pdb=" CA  LYS A 134 "
        pdb=" C   LYS A 134 "
      ideal   model   delta    sigma   weight residual
     114.09  108.43    5.66 1.55e+00 4.16e-01 1.33e+01
  angle pdb=" C   GLY C 261 "
        pdb=" N   GLY C 262 "
        pdb=" CA  GLY C 262 "
      ideal   model   delta    sigma   weight residual
     120.03  123.89   -3.86 1.12e+00 7.97e-01 1.19e+01
  angle pdb=" C   LEU A   9 "
        pdb=" N   PHE A  10 "
        pdb=" CA  PHE A  10 "
      ideal   model   delta    sigma   weight residual
     121.80  130.10   -8.30 2.44e+00 1.68e-01 1.16e+01
  angle pdb=" N   ARG B  68 "
        pdb=" CA  ARG B  68 "
        pdb=" C   ARG B  68 "
      ideal   model   delta    sigma   weight residual
     113.18  108.70    4.48 1.33e+00 5.65e-01 1.14e+01
  ... (remaining 9298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3732
       17.94 -    35.88: 400
       35.88 -    53.83: 49
       53.83 -    71.77: 17
       71.77 -    89.71: 11
  Dihedral angle restraints: 4209
    sinusoidal: 1713
      harmonic: 2496
  Sorted by residual:
  dihedral pdb=" CA  GLU C   8 "
           pdb=" C   GLU C   8 "
           pdb=" N   GLY C   9 "
           pdb=" CA  GLY C   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.07   25.93     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  LEU A   9 "
           pdb=" C   LEU A   9 "
           pdb=" N   PHE A  10 "
           pdb=" CA  PHE A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.50  -25.50     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  ALA C 184 "
           pdb=" C   ALA C 184 "
           pdb=" N   LYS C 185 "
           pdb=" CA  LYS C 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.53  -24.47     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 4206 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 865
       0.056 -    0.113: 180
       0.113 -    0.169: 26
       0.169 -    0.226: 1
       0.226 -    0.282: 1
  Chirality restraints: 1073
  Sorted by residual:
  chirality pdb=" CB  ILE B 189 "
            pdb=" CA  ILE B 189 "
            pdb=" CG1 ILE B 189 "
            pdb=" CG2 ILE B 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CG  LEU B 142 "
            pdb=" CB  LEU B 142 "
            pdb=" CD1 LEU B 142 "
            pdb=" CD2 LEU B 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CG  LEU D 129 "
            pdb=" CB  LEU D 129 "
            pdb=" CD1 LEU D 129 "
            pdb=" CD2 LEU D 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.15e-01
  ... (remaining 1070 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  50 "   -0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO A  51 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  51 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  51 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B  69 "    0.033 5.00e-02 4.00e+02   5.03e-02 4.05e+00
        pdb=" N   PRO B  70 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B  70 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  70 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 239 "    0.010 2.00e-02 2.50e+03   2.00e-02 4.00e+00
        pdb=" C   ALA C 239 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ALA C 239 "    0.013 2.00e-02 2.50e+03
        pdb=" N   MET C 240 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 171
        2.66 -     3.22: 6936
        3.22 -     3.78: 10675
        3.78 -     4.34: 14263
        4.34 -     4.90: 22290
  Nonbonded interactions: 54335
  Sorted by model distance:
  nonbonded pdb=" O   LYS C  78 "
            pdb=" OG1 THR C 321 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   LYS C  13 "
            pdb=" NE2 HIS C  49 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" OE2 GLU C   8 "
            pdb=" OG  SER C  10 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OD1 ASN D 122 "
            pdb=" NE2 GLN D 126 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OE2 GLU B  44 "
            pdb=" NH1 ARG B  80 "
     model   vdw
     2.180 3.120
  ... (remaining 54330 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     7.860
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5533
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   0.040   6883  Z= 0.191
  Angle     :  0.820   8.297   9303  Z= 0.483
  Chirality :  0.045   0.282   1073
  Planarity :  0.005   0.057   1206
  Dihedral  : 15.377  89.712   2599
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 20.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.01 %
    Favored  : 94.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -4.80 (0.23), residues: 862
  helix: -2.94 (0.20), residues: 353
  sheet: -1.86 (0.47), residues: 98
  loop : -3.79 (0.25), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  94 
 TYR   0.015   0.002   TYR C 324 
 PHE   0.021   0.002   PHE B  63 
 TRP   0.009   0.001   TRP C 333 
 HIS   0.009   0.002   HIS C  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6883)
  covalent geometry    : angle       0.82047 ( 9303)
  hydrogen bonds       : bond        0.16544 (  350)
  hydrogen bonds       : angle       7.90923 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.177 
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: A   70 MET cc_start: 0.5039 (ptt) cc_final: 0.4534 (ptp)
REVERT: B  201 TYR cc_start: 0.8054 (t80) cc_final: 0.7762 (t80)
REVERT: C  218 MET cc_start: 0.0784 (tmm) cc_final: 0.0336 (ttp)
REVERT: D  116 LEU cc_start: 0.8579 (tt) cc_final: 0.8321 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0869
  time to fit residues: 15.5497
Evaluate side-chains
  97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A  86 ASN
A 116 GLN
B  41 GLN
B  53 GLN
B  69 HIS
B 141 ASN
B 148 GLN
** C  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 179 ASN
C 216 HIS
C 270 GLN
** D  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.095042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.077501 restraints weight = 47254.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.078648 restraints weight = 39459.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.079359 restraints weight = 34165.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.080092 restraints weight = 31104.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.080552 restraints weight = 28751.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6883  Z= 0.171
  Angle     :  0.739   8.807   9303  Z= 0.383
  Chirality :  0.045   0.170   1073
  Planarity :  0.006   0.052   1206
  Dihedral  :  6.596  45.505    949
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.56 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -3.17 (0.26), residues: 862
  helix: -1.23 (0.24), residues: 384
  sheet: -1.30 (0.50), residues: 98
  loop : -3.30 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  18 
 TYR   0.014   0.002   TYR E   7 
 PHE   0.013   0.002   PHE D  69 
 TRP   0.008   0.001   TRP D 108 
 HIS   0.007   0.002   HIS C  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6883)
  covalent geometry    : angle       0.73921 ( 9303)
  hydrogen bonds       : bond        0.04947 (  350)
  hydrogen bonds       : angle       6.43901 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.308 
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: A   20 PHE cc_start: 0.8957 (m-80) cc_final: 0.8613 (t80)
REVERT: A   70 MET cc_start: 0.8763 (ptt) cc_final: 0.8537 (ptp)
REVERT: B  130 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7225 (tpt)
REVERT: C  272 MET cc_start: 0.2713 (OUTLIER) cc_final: 0.2314 (mtt)
REVERT: E   40 MET cc_start: 0.9279 (ptt) cc_final: 0.9026 (ptt)
  outliers start: 23
  outliers final: 10
  residues processed: 122
  average time/residue: 0.0830
  time to fit residues: 13.4197
Evaluate side-chains
  98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  113 HIS
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain C residue  273 MET
Chi-restraints excluded: chain C residue  284 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 67 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 52 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 78 optimal weight:   20.0000
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
B  61 HIS
B 109 ASN
** C  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.091624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.072653 restraints weight = 43999.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.073541 restraints weight = 38532.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.074129 restraints weight = 35322.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.074420 restraints weight = 32923.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.074864 restraints weight = 31615.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6883  Z= 0.180
  Angle     :  0.732  12.112   9303  Z= 0.374
  Chirality :  0.045   0.163   1073
  Planarity :  0.005   0.049   1206
  Dihedral  :  6.406  42.062    949
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 20.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.54 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.52 (0.27), residues: 862
  helix: -0.66 (0.25), residues: 394
  sheet: -0.88 (0.52), residues: 97
  loop : -3.07 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 247 
 TYR   0.014   0.002   TYR C 141 
 PHE   0.013   0.002   PHE D 123 
 TRP   0.008   0.001   TRP C 333 
 HIS   0.006   0.002   HIS C  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6883)
  covalent geometry    : angle       0.73226 ( 9303)
  hydrogen bonds       : bond        0.04798 (  350)
  hydrogen bonds       : angle       6.13948 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.277 
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: A  169 MET cc_start: 0.7670 (ttt) cc_final: 0.6753 (tpt)
REVERT: C  272 MET cc_start: 0.2784 (mtt) cc_final: 0.2470 (mtt)
REVERT: D  117 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8543 (tpp80)
REVERT: E   40 MET cc_start: 0.9175 (ptt) cc_final: 0.8883 (ptt)
  outliers start: 25
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0760
  time to fit residues: 11.0704
Evaluate side-chains
  94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  113 HIS
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  200 MET
Chi-restraints excluded: chain C residue  270 GLN
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain D residue  117 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 10 optimal weight:   30.0000
   chunk 12 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A 116 GLN
** C  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.090593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.071508 restraints weight = 44494.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.072438 restraints weight = 39330.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.072858 restraints weight = 35544.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.073478 restraints weight = 33666.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.073665 restraints weight = 31907.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6883  Z= 0.170
  Angle     :  0.703   9.753   9303  Z= 0.358
  Chirality :  0.045   0.168   1073
  Planarity :  0.005   0.045   1206
  Dihedral  :  6.197  38.604    949
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 19.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.57 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -2.08 (0.28), residues: 862
  helix: -0.16 (0.25), residues: 396
  sheet: -1.07 (0.53), residues: 101
  loop : -2.90 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 163 
 TYR   0.018   0.002   TYR C 195 
 PHE   0.010   0.002   PHE C 307 
 TRP   0.015   0.002   TRP D 108 
 HIS   0.005   0.001   HIS C  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6883)
  covalent geometry    : angle       0.70328 ( 9303)
  hydrogen bonds       : bond        0.04501 (  350)
  hydrogen bonds       : angle       5.93312 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.180 
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: A   20 PHE cc_start: 0.8909 (m-80) cc_final: 0.8516 (t80)
REVERT: A   70 MET cc_start: 0.8844 (ptt) cc_final: 0.7413 (ptp)
REVERT: A  169 MET cc_start: 0.7704 (ttt) cc_final: 0.7453 (mmm)
REVERT: C  116 MET cc_start: 0.8564 (mmm) cc_final: 0.8206 (mmm)
REVERT: C  162 ASP cc_start: 0.9241 (m-30) cc_final: 0.8613 (t0)
REVERT: C  183 MET cc_start: 0.8751 (tmm) cc_final: 0.8443 (tmm)
REVERT: C  200 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.5219 (mmm)
REVERT: C  272 MET cc_start: 0.2695 (OUTLIER) cc_final: 0.2428 (mtt)
REVERT: D  117 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8249 (mmm160)
REVERT: D  125 ASP cc_start: 0.9625 (m-30) cc_final: 0.9178 (m-30)
REVERT: D  134 MET cc_start: 0.5885 (ttm) cc_final: 0.5678 (ttm)
REVERT: E   40 MET cc_start: 0.9137 (ptt) cc_final: 0.8727 (ptt)
  outliers start: 28
  outliers final: 17
  residues processed: 106
  average time/residue: 0.0645
  time to fit residues: 9.3685
Evaluate side-chains
  99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  221 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  113 HIS
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  200 MET
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain D residue  116 LEU
Chi-restraints excluded: chain D residue  117 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0060
   chunk 56 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0770
   chunk 61 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.0158

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
B 141 ASN
C  12 ASN
C  69 GLN
** D  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.094180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.076703 restraints weight = 48075.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.077832 restraints weight = 40568.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.078469 restraints weight = 35727.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.079153 restraints weight = 32821.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.079441 restraints weight = 30460.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6883  Z= 0.133
  Angle     :  0.706  10.390   9303  Z= 0.352
  Chirality :  0.045   0.176   1073
  Planarity :  0.004   0.044   1206
  Dihedral  :  5.864  36.015    949
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 16.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.65 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -1.58 (0.28), residues: 862
  helix:  0.30 (0.25), residues: 399
  sheet: -0.91 (0.52), residues: 110
  loop : -2.74 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  18 
 TYR   0.013   0.002   TYR C 141 
 PHE   0.014   0.001   PHE D  69 
 TRP   0.017   0.002   TRP D 108 
 HIS   0.005   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6883)
  covalent geometry    : angle       0.70563 ( 9303)
  hydrogen bonds       : bond        0.04006 (  350)
  hydrogen bonds       : angle       5.59744 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8928 (m-80) cc_final: 0.8544 (t80)
REVERT: A   70 MET cc_start: 0.7854 (ptt) cc_final: 0.7102 (ptp)
REVERT: A  169 MET cc_start: 0.7568 (ttt) cc_final: 0.7349 (mmm)
REVERT: C    7 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.6880 (t80)
REVERT: C  116 MET cc_start: 0.8556 (mmm) cc_final: 0.8184 (mmm)
REVERT: C  162 ASP cc_start: 0.9265 (m-30) cc_final: 0.8644 (t0)
REVERT: C  240 MET cc_start: 0.6976 (mmm) cc_final: 0.6776 (mmm)
REVERT: C  272 MET cc_start: 0.2641 (mtt) cc_final: 0.1808 (mtt)
REVERT: D  117 ARG cc_start: 0.8754 (tpp80) cc_final: 0.7902 (mmm-85)
REVERT: D  125 ASP cc_start: 0.9627 (m-30) cc_final: 0.9211 (t0)
REVERT: E   40 MET cc_start: 0.9174 (ptt) cc_final: 0.8761 (ptt)
  outliers start: 21
  outliers final: 9
  residues processed: 105
  average time/residue: 0.0622
  time to fit residues: 9.0340
Evaluate side-chains
  93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain C residue    7 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  284 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A 116 GLN
B 211 HIS
C 135 ASN
D  89 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.093420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.076075 restraints weight = 48454.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.077230 restraints weight = 40719.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.078084 restraints weight = 35491.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.078669 restraints weight = 32069.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.078948 restraints weight = 29847.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6883  Z= 0.136
  Angle     :  0.694  10.361   9303  Z= 0.346
  Chirality :  0.044   0.166   1073
  Planarity :  0.005   0.043   1206
  Dihedral  :  5.742  34.571    949
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 21.38 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -1.30 (0.28), residues: 862
  helix:  0.55 (0.25), residues: 397
  sheet: -0.62 (0.51), residues: 113
  loop : -2.67 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.012   0.002   TYR C 141 
 PHE   0.012   0.001   PHE B  63 
 TRP   0.014   0.002   TRP D 108 
 HIS   0.006   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6883)
  covalent geometry    : angle       0.69351 ( 9303)
  hydrogen bonds       : bond        0.03911 (  350)
  hydrogen bonds       : angle       5.50025 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.180 
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: A   20 PHE cc_start: 0.8963 (m-80) cc_final: 0.8589 (t80)
REVERT: A   70 MET cc_start: 0.7831 (ptt) cc_final: 0.7050 (ptp)
REVERT: A  169 MET cc_start: 0.7612 (ttt) cc_final: 0.7305 (mmm)
REVERT: B  142 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7273 (tp)
REVERT: C    7 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6751 (t80)
REVERT: C  116 MET cc_start: 0.8564 (mmm) cc_final: 0.8166 (mmm)
REVERT: D  117 ARG cc_start: 0.8748 (tpp80) cc_final: 0.7898 (mmm-85)
REVERT: D  125 ASP cc_start: 0.9620 (m-30) cc_final: 0.9217 (t0)
REVERT: E   15 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8811 (mm110)
REVERT: E   40 MET cc_start: 0.9201 (ptt) cc_final: 0.8768 (ptt)
  outliers start: 25
  outliers final: 14
  residues processed: 104
  average time/residue: 0.0620
  time to fit residues: 8.8635
Evaluate side-chains
  96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain C residue    7 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  113 HIS
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  233 LEU
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain D residue  116 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   chunk 39 optimal weight:   20.0000
   chunk 67 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A 116 GLN
E  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.093268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.076029 restraints weight = 47396.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.077163 restraints weight = 39220.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.077661 restraints weight = 34269.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.078467 restraints weight = 31701.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.078937 restraints weight = 29259.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6774
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6883  Z= 0.137
  Angle     :  0.718  10.497   9303  Z= 0.357
  Chirality :  0.044   0.166   1073
  Planarity :  0.004   0.042   1206
  Dihedral  :  5.661  33.978    949
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.06 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -1.14 (0.29), residues: 862
  helix:  0.64 (0.26), residues: 398
  sheet: -0.57 (0.51), residues: 114
  loop : -2.54 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 117 
 TYR   0.012   0.002   TYR C 141 
 PHE   0.012   0.001   PHE B  63 
 TRP   0.011   0.002   TRP D 108 
 HIS   0.007   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6883)
  covalent geometry    : angle       0.71839 ( 9303)
  hydrogen bonds       : bond        0.03842 (  350)
  hydrogen bonds       : angle       5.46878 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 MET cc_start: 0.9116 (ptp) cc_final: 0.8806 (pmm)
REVERT: A   70 MET cc_start: 0.7741 (ptt) cc_final: 0.6994 (ptp)
REVERT: A  169 MET cc_start: 0.7614 (ttt) cc_final: 0.7252 (mmm)
REVERT: B  130 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7059 (tpt)
REVERT: B  142 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7294 (tp)
REVERT: C    7 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.6728 (t80)
REVERT: C  116 MET cc_start: 0.8591 (mmm) cc_final: 0.8182 (mmm)
REVERT: C  183 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8324 (tmm)
REVERT: D  117 ARG cc_start: 0.8747 (tpp80) cc_final: 0.7869 (mmm-85)
REVERT: D  125 ASP cc_start: 0.9618 (m-30) cc_final: 0.9137 (t0)
REVERT: D  134 MET cc_start: 0.5872 (ttm) cc_final: 0.5562 (tpp)
REVERT: E   40 MET cc_start: 0.9216 (ptt) cc_final: 0.8847 (ptt)
  outliers start: 23
  outliers final: 16
  residues processed: 99
  average time/residue: 0.0656
  time to fit residues: 8.9452
Evaluate side-chains
  100 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  221 PHE
Chi-restraints excluded: chain C residue    7 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  113 HIS
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain D residue  116 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 35 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 68 optimal weight:   30.0000
   chunk 36 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A 116 GLN
** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.088555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.071337 restraints weight = 49052.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.072404 restraints weight = 40900.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.073205 restraints weight = 36005.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 14)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.073557 restraints weight = 32671.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.074076 restraints weight = 30844.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   6883  Z= 0.249
  Angle     :  0.841  14.463   9303  Z= 0.425
  Chirality :  0.047   0.177   1073
  Planarity :  0.005   0.044   1206
  Dihedral  :  6.172  36.158    949
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 24.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 22.06 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -1.75 (0.28), residues: 862
  helix: -0.05 (0.25), residues: 397
  sheet: -0.73 (0.52), residues: 114
  loop : -2.64 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 247 
 TYR   0.015   0.003   TYR B 201 
 PHE   0.012   0.002   PHE C 210 
 TRP   0.006   0.001   TRP C 333 
 HIS   0.008   0.002   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 6883)
  covalent geometry    : angle       0.84145 ( 9303)
  hydrogen bonds       : bond        0.05109 (  350)
  hydrogen bonds       : angle       5.93205 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.9000 (m-80) cc_final: 0.8635 (t80)
REVERT: A   34 MET cc_start: 0.9153 (ptp) cc_final: 0.8947 (ptp)
REVERT: A   70 MET cc_start: 0.7833 (ptt) cc_final: 0.7086 (ptp)
REVERT: A  169 MET cc_start: 0.7894 (ttt) cc_final: 0.7281 (mmm)
REVERT: C  116 MET cc_start: 0.8488 (mmm) cc_final: 0.8070 (mmm)
REVERT: D  117 ARG cc_start: 0.8692 (tpp80) cc_final: 0.7902 (mmm-85)
REVERT: D  125 ASP cc_start: 0.9648 (m-30) cc_final: 0.9176 (t0)
REVERT: D  134 MET cc_start: 0.6271 (ttm) cc_final: 0.5976 (tpp)
REVERT: E   15 GLN cc_start: 0.8997 (mm110) cc_final: 0.8790 (mm110)
REVERT: E   40 MET cc_start: 0.9180 (ptt) cc_final: 0.8758 (ptt)
  outliers start: 28
  outliers final: 20
  residues processed: 100
  average time/residue: 0.0514
  time to fit residues: 7.3176
Evaluate side-chains
  99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  221 PHE
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  113 HIS
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain D residue  116 LEU
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain E residue   39 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 61 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 68 optimal weight:   30.0000
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 82 optimal weight:   20.0000
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
E  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.089988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.072947 restraints weight = 48345.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.074010 restraints weight = 40693.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.074498 restraints weight = 35752.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.075257 restraints weight = 32948.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.075552 restraints weight = 30541.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6883  Z= 0.171
  Angle     :  0.791  13.419   9303  Z= 0.393
  Chirality :  0.047   0.329   1073
  Planarity :  0.005   0.042   1206
  Dihedral  :  6.042  35.331    949
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 21.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 22.33 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -1.48 (0.28), residues: 862
  helix:  0.22 (0.25), residues: 396
  sheet: -0.75 (0.52), residues: 115
  loop : -2.48 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 247 
 TYR   0.014   0.002   TYR C 141 
 PHE   0.017   0.002   PHE D  69 
 TRP   0.009   0.001   TRP D 108 
 HIS   0.009   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6883)
  covalent geometry    : angle       0.79083 ( 9303)
  hydrogen bonds       : bond        0.04462 (  350)
  hydrogen bonds       : angle       5.74586 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8991 (m-80) cc_final: 0.8611 (t80)
REVERT: A   34 MET cc_start: 0.9171 (ptp) cc_final: 0.8953 (ptp)
REVERT: A   70 MET cc_start: 0.7786 (ptt) cc_final: 0.6912 (ptp)
REVERT: A  169 MET cc_start: 0.7763 (ttt) cc_final: 0.7474 (mmm)
REVERT: C  116 MET cc_start: 0.8494 (mmm) cc_final: 0.8067 (mmm)
REVERT: C  183 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8319 (tmm)
REVERT: C  272 MET cc_start: 0.2445 (mtt) cc_final: 0.1982 (mtt)
REVERT: D  117 ARG cc_start: 0.8729 (tpp80) cc_final: 0.7962 (mmm-85)
REVERT: D  125 ASP cc_start: 0.9624 (m-30) cc_final: 0.9158 (t0)
REVERT: D  134 MET cc_start: 0.6065 (ttm) cc_final: 0.5801 (tpp)
REVERT: E   40 MET cc_start: 0.9134 (ptt) cc_final: 0.8720 (ptt)
  outliers start: 24
  outliers final: 21
  residues processed: 99
  average time/residue: 0.0635
  time to fit residues: 8.8642
Evaluate side-chains
  101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain B residue   48 PHE
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  221 PHE
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  113 HIS
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain D residue  116 LEU
Chi-restraints excluded: chain E residue   39 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    0.0170
   chunk 47 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 76 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
E  15 GLN
E  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.091902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.073341 restraints weight = 43353.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.074295 restraints weight = 37235.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.074709 restraints weight = 33494.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.075405 restraints weight = 31555.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.075816 restraints weight = 29719.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6883  Z= 0.130
  Angle     :  0.774  12.207   9303  Z= 0.379
  Chirality :  0.046   0.205   1073
  Planarity :  0.004   0.045   1206
  Dihedral  :  5.737  32.790    949
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 23.55 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -1.11 (0.29), residues: 862
  helix:  0.52 (0.26), residues: 397
  sheet: -0.67 (0.51), residues: 114
  loop : -2.26 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 117 
 TYR   0.012   0.001   TYR C 141 
 PHE   0.012   0.001   PHE D  69 
 TRP   0.012   0.001   TRP D 108 
 HIS   0.008   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6883)
  covalent geometry    : angle       0.77408 ( 9303)
  hydrogen bonds       : bond        0.03835 (  350)
  hydrogen bonds       : angle       5.44511 ( 1014)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8939 (m-80) cc_final: 0.8525 (t80)
REVERT: A   34 MET cc_start: 0.9139 (ptp) cc_final: 0.8923 (ptp)
REVERT: A   70 MET cc_start: 0.7710 (ptt) cc_final: 0.6961 (ptp)
REVERT: A  169 MET cc_start: 0.7540 (ttt) cc_final: 0.6976 (mmm)
REVERT: B  130 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7560 (tpp)
REVERT: C  116 MET cc_start: 0.8557 (mmm) cc_final: 0.8164 (mmm)
REVERT: C  183 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8371 (tmm)
REVERT: D  116 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8415 (pp)
REVERT: D  117 ARG cc_start: 0.8846 (tpp80) cc_final: 0.8393 (mmm160)
REVERT: D  125 ASP cc_start: 0.9598 (m-30) cc_final: 0.9238 (t0)
REVERT: D  134 MET cc_start: 0.5835 (ttm) cc_final: 0.5542 (tpp)
REVERT: E   40 MET cc_start: 0.9203 (ptt) cc_final: 0.8764 (ptt)
  outliers start: 18
  outliers final: 13
  residues processed: 99
  average time/residue: 0.0598
  time to fit residues: 8.1998
Evaluate side-chains
  97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue  113 HIS
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  144 HIS
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain D residue  116 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 65 optimal weight:   10.0000
   chunk 11 optimal weight:   30.0000
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   chunk 14 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
** C 278 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 = 0.4267 r_free = 0.4267 target = 0.092550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.075253 restraints weight = 47221.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.076381 restraints weight = 39282.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.077206 restraints weight = 34379.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.077580 restraints weight = 31168.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.078168 restraints weight = 29325.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.5062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6883  Z= 0.138
  Angle     :  0.810  16.237   9303  Z= 0.395
  Chirality :  0.046   0.208   1073
  Planarity :  0.005   0.051   1206
  Dihedral  :  5.636  32.643    949
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 24.22 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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 are not related in a simple way.
  whole: -1.02 (0.29), residues: 862
  helix:  0.54 (0.26), residues: 394
  sheet: -0.54 (0.51), residues: 114
  loop : -2.15 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 247 
 TYR   0.012   0.002   TYR C 141 
 PHE   0.019   0.001   PHE D  69 
 TRP   0.010   0.001   TRP D 108 
 HIS   0.008   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6883)
  covalent geometry    : angle       0.81015 ( 9303)
  hydrogen bonds       : bond        0.03971 (  350)
  hydrogen bonds       : angle       5.49815 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1276.39 seconds
wall clock time: 22 minutes 44.74 seconds (1364.74 seconds total)