Starting phenix.real_space_refine
on Wed Jan 15 19:59:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyv_60580/01_2025/8zyv_60580.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyv_60580/01_2025/8zyv_60580.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyv_60580/01_2025/8zyv_60580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyv_60580/01_2025/8zyv_60580.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyv_60580/01_2025/8zyv_60580.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyv_60580/01_2025/8zyv_60580.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      77      5.16       5
     Na      2      4.78       5
     C    5741      2.51       5
     N    1469      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8913
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 361
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "B"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 368
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "C"
      Number of atoms: 1601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1601
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1621
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 6, 'TRANS': 207}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1729
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' NA': 2}
          Classifications: {'undetermined': 2, 'water': 2}
          Link IDs: {None: 3}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb="NA    NA A 502 " occ=0.97
    residue:
      pdb=" O   HOH A 601 " occ=0.65
    residue:
      pdb=" O   HOH E 602 " occ=0.97
    residue:
      pdb=" O   HOH G 301 " occ=0.42
  Time building chain proxies: 5.20, per 1000 atoms: 0.58
  Number of scatterers: 8913
  At special positions: 0
  Unit cell: (102.6, 98.55, 105.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      77     16.00
     Na      2     11.00
     O    1624      8.00
     N    1469      7.00
     C    5741      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 1 sheets defined
      91.3% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.877A  pdb=" N   GLY A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 59
    Processing helix  chain 'B' and resid 18 through 39
      removed outlier: 3.956A  pdb=" N   PHE B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 58
    Processing helix  chain 'C' and resid 31 through 50
    Processing helix  chain 'C' and resid 51 through 68
    Processing helix  chain 'C' and resid 72 through 87
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.974A  pdb=" N   ASP C 114 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 167
      removed outlier: 3.639A  pdb=" N   VAL C 121 " --> pdb=" O   ASP C 117 " (cutoff:3.500A)
      Proline residue:  C 151  - end of helix
    Processing helix  chain 'C' and resid 171 through 173
      No H-bonds generated for 'chain 'C' and resid 171 through 173'
    Processing helix  chain 'C' and resid 174 through 195
      removed outlier: 3.939A  pdb=" N   MET C 179 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ALA C 180 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL C 181 " --> pdb=" O   PRO C 177 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR C 185 " --> pdb=" O   VAL C 181 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   THR C 186 " --> pdb=" O   ALA C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 228
    Processing helix  chain 'C' and resid 230 through 240
    Processing helix  chain 'D' and resid 31 through 47
    Processing helix  chain 'D' and resid 51 through 68
    Processing helix  chain 'D' and resid 72 through 87
      removed outlier: 3.964A  pdb=" N   ASP D  85 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ALA D  86 " --> pdb=" O   GLU D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 115
    Processing helix  chain 'D' and resid 117 through 167
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 175 through 196
      removed outlier: 3.734A  pdb=" N   VAL D 181 " --> pdb=" O   PRO D 177 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ALA D 182 " --> pdb=" O   ALA D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 228
    Processing helix  chain 'D' and resid 230 through 239
      removed outlier: 4.293A  pdb=" N   ILE D 234 " --> pdb=" O   ASN D 230 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ASP D 235 " --> pdb=" O   PRO D 231 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   SER D 236 " --> pdb=" O   ARG D 232 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   TYR D 237 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LYS D 239 " --> pdb=" O   ASP D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 250
      removed outlier: 3.556A  pdb=" N   ARG D 247 " --> pdb=" O   GLU D 244 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU D 249 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 48
      removed outlier: 3.565A  pdb=" N   ASP E  31 " --> pdb=" O   GLY E  27 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 68
    Processing helix  chain 'E' and resid 72 through 87
    Processing helix  chain 'E' and resid 102 through 114
    Processing helix  chain 'E' and resid 117 through 168
      Proline residue:  E 151  - end of helix
    Processing helix  chain 'E' and resid 171 through 196
      removed outlier: 3.807A  pdb=" N   GLY E 176 " --> pdb=" O   PRO E 172 " (cutoff:3.500A)
      Proline residue:  E 177  - end of helix
    Processing helix  chain 'E' and resid 196 through 228
    Processing helix  chain 'E' and resid 230 through 240
    Processing helix  chain 'E' and resid 241 through 248
      removed outlier: 6.723A  pdb=" N   GLY E 245 " --> pdb=" O   LEU E 242 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   LYS E 246 " --> pdb=" O   ASN E 243 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA E 248 " --> pdb=" O   GLY E 245 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 23
    Processing helix  chain 'F' and resid 32 through 47
      removed outlier: 3.564A  pdb=" N   VAL F  38 " --> pdb=" O   SER F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 68
    Processing helix  chain 'F' and resid 72 through 87
    Processing helix  chain 'F' and resid 102 through 115
      removed outlier: 3.866A  pdb=" N   GLY F 115 " --> pdb=" O   LEU F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 117 through 168
      Proline residue:  F 151  - end of helix
    Processing helix  chain 'F' and resid 171 through 173
      No H-bonds generated for 'chain 'F' and resid 171 through 173'
    Processing helix  chain 'F' and resid 174 through 196
      removed outlier: 3.686A  pdb=" N   THR F 185 " --> pdb=" O   VAL F 181 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   THR F 186 " --> pdb=" O   ALA F 182 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   MET F 195 " --> pdb=" O   ILE F 191 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 228
    Processing helix  chain 'F' and resid 230 through 243
    Processing helix  chain 'F' and resid 244 through 251
      removed outlier: 3.546A  pdb=" N   ARG F 247 " --> pdb=" O   GLU F 244 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 50
    Processing helix  chain 'G' and resid 51 through 67
    Processing helix  chain 'G' and resid 72 through 87
    Processing helix  chain 'G' and resid 102 through 113
    Processing helix  chain 'G' and resid 117 through 169
      removed outlier: 4.142A  pdb=" N   VAL G 121 " --> pdb=" O   ASP G 117 " (cutoff:3.500A)
      Proline residue:  G 151  - end of helix
    Processing helix  chain 'G' and resid 171 through 196
      removed outlier: 3.564A  pdb=" N   GLY G 176 " --> pdb=" O   PRO G 172 " (cutoff:3.500A)
      Proline residue:  G 177  - end of helix
    Processing helix  chain 'G' and resid 196 through 228
    Processing helix  chain 'G' and resid 230 through 238
    Processing helix  chain 'G' and resid 238 through 243
      removed outlier: 3.611A  pdb=" N   ASN G 243 " --> pdb=" O   LYS G 239 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 244 through 250
      removed outlier: 3.659A  pdb=" N   ARG G 247 " --> pdb=" O   GLU G 244 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42

    815 hydrogen bonds defined for protein.
    2412 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.39

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2896
        1.35 -     1.46: 1873
        1.46 -     1.58: 4108
        1.58 -     1.70: 0
        1.70 -     1.82: 152
  Bond restraints: 9029
  Sorted by residual:
  bond pdb=" CB  MET C 179 "
       pdb=" CG  MET C 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.484  0.036 3.00e-02 1.11e+03 1.47e+00
  bond pdb=" CG  MET C 179 "
       pdb=" SD  MET C 179 "
    ideal  model  delta    sigma   weight residual
    1.803  1.773  0.030 2.50e-02 1.60e+03 1.46e+00
  bond pdb=" CB  ASP G  75 "
       pdb=" CG  ASP G  75 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.93e-01
  bond pdb=" CB  ILE D  61 "
       pdb=" CG1 ILE D  61 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 2.00e-02 2.50e+03 6.64e-01
  bond pdb=" CA  PRO D 172 "
       pdb=" CB  PRO D 172 "
    ideal  model  delta    sigma   weight residual
    1.532  1.537 -0.006 7.10e-03 1.98e+04 6.59e-01
  ... (remaining 9024 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 11943
        1.47 -     2.94: 158
        2.94 -     4.41: 45
        4.41 -     5.88: 12
        5.88 -     7.35: 2
  Bond angle restraints: 12160
  Sorted by residual:
  angle pdb=" CG  MET C 179 "
        pdb=" SD  MET C 179 "
        pdb=" CE  MET C 179 "
      ideal   model   delta    sigma   weight residual
     100.90   94.42    6.48 2.20e+00 2.07e-01 8.68e+00
  angle pdb=" N   MET F  67 "
        pdb=" CA  MET F  67 "
        pdb=" C   MET F  67 "
      ideal   model   delta    sigma   weight residual
     111.03  113.90   -2.87 1.11e+00 8.12e-01 6.70e+00
  angle pdb=" N   GLY E 245 "
        pdb=" CA  GLY E 245 "
        pdb=" C   GLY E 245 "
      ideal   model   delta    sigma   weight residual
     110.86  115.21   -4.35 1.84e+00 2.95e-01 5.58e+00
  angle pdb=" CA  MET D 105 "
        pdb=" CB  MET D 105 "
        pdb=" CG  MET D 105 "
      ideal   model   delta    sigma   weight residual
     114.10  118.38   -4.28 2.00e+00 2.50e-01 4.58e+00
  angle pdb=" CA  LEU D 213 "
        pdb=" CB  LEU D 213 "
        pdb=" CG  LEU D 213 "
      ideal   model   delta    sigma   weight residual
     116.30  123.65   -7.35 3.50e+00 8.16e-02 4.41e+00
  ... (remaining 12155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 4572
       17.50 -    35.00: 636
       35.00 -    52.50: 194
       52.50 -    70.00: 31
       70.00 -    87.50: 10
  Dihedral angle restraints: 5443
    sinusoidal: 2129
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CA  ASP F 220 "
           pdb=" CB  ASP F 220 "
           pdb=" CG  ASP F 220 "
           pdb=" OD1 ASP F 220 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.57   57.57     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ASP D 133 "
           pdb=" CB  ASP D 133 "
           pdb=" CG  ASP D 133 "
           pdb=" OD1 ASP D 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.01   57.01     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  ASP E  85 "
           pdb=" CB  ASP E  85 "
           pdb=" CG  ASP E  85 "
           pdb=" OD1 ASP E  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.26   55.26     1      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 5440 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 931
       0.027 -    0.054: 317
       0.054 -    0.081: 150
       0.081 -    0.108: 39
       0.108 -    0.135: 9
  Chirality restraints: 1446
  Sorted by residual:
  chirality pdb=" CA  ASP C 148 "
            pdb=" N   ASP C 148 "
            pdb=" C   ASP C 148 "
            pdb=" CB  ASP C 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" CA  ASP E 148 "
            pdb=" N   ASP E 148 "
            pdb=" C   ASP E 148 "
            pdb=" CB  ASP E 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CG  LEU D 166 "
            pdb=" CB  LEU D 166 "
            pdb=" CD1 LEU D 166 "
            pdb=" CD2 LEU D 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.47   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 1443 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 180 "   -0.009 2.00e-02 2.50e+03   1.84e-02 3.37e+00
        pdb=" C   ALA C 180 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ALA C 180 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL C 181 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  15 "   -0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO B  16 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE G  37 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.73e+00
        pdb=" C   ILE G  37 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE G  37 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL G  38 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 210
        2.72 -     3.26: 9197
        3.26 -     3.81: 15322
        3.81 -     4.35: 17308
        4.35 -     4.90: 30752
  Nonbonded interactions: 72789
  Sorted by model distance:
  nonbonded pdb=" O   PHE D  29 "
            pdb=" OH  TYR D 188 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OG1 THR E 158 "
            pdb=" OG1 THR E 186 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   LEU A  35 "
            pdb=" OG  SER A  38 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OD1 ASP E  31 "
            pdb=" OH  TYR E 188 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   VAL F  38 "
            pdb=" OG  SER F  42 "
     model   vdw
     2.318 3.040
  ... (remaining 72784 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 14 through 59)
  selection = (chain 'B' and resid 14 through 59)
}
ncs_group {
  reference = (chain 'C' and resid 29 through 250)
  selection = (chain 'D' and resid 29 through 250)
  selection = (chain 'E' and resid 29 through 250)
  selection = (chain 'F' and (resid 15 through 16 or resid 31 through 250))
  selection = (chain 'G' and resid 29 through 250)
}

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=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.200
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.190
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
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      :  0.003   0.036   9029  Z= 0.166
  Angle     :  0.488   7.347  12160  Z= 0.259
  Chirality :  0.035   0.135   1446
  Planarity :  0.004   0.045   1543
  Dihedral  : 17.749  87.504   3305
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 27.98 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.33 (0.25), residues: 1148
  helix:  2.57 (0.16), residues: 998
  sheet:  None (None), residues: 0
  loop : -0.47 (0.51), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  18 
 HIS   0.002   0.000   HIS E 136 
 PHE   0.019   0.001   PHE A  32 
 TYR   0.014   0.001   TYR F 241 
 ARG   0.005   0.000   ARG G 215 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.936 
Fit side-chains
REVERT: C  149 VAL cc_start: 0.8627 (p) cc_final: 0.8422 (t)
REVERT: D   75 ASP cc_start: 0.7664 (m-30) cc_final: 0.7139 (t70)
REVERT: F   67 MET cc_start: 0.8345 (mtm) cc_final: 0.8119 (mtm)
REVERT: G   75 ASP cc_start: 0.7105 (t0) cc_final: 0.6798 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 154
  average time/residue: 0.2322
  time to fit residues: 48.1725
Evaluate side-chains
  152 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain F residue   51 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.178421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.112614 restraints weight = 8812.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.62
r_work: 0.2952 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.0863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9029  Z= 0.268
  Angle     :  0.501   7.121  12160  Z= 0.263
  Chirality :  0.038   0.129   1446
  Planarity :  0.004   0.047   1543
  Dihedral  :  3.814  40.018   1224
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 25.85 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.40 (0.25), residues: 1148
  helix:  2.59 (0.16), residues: 1011
  sheet:  None (None), residues: 0
  loop : -0.57 (0.51), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B  18 
 HIS   0.005   0.001   HIS G 136 
 PHE   0.022   0.002   PHE A  32 
 TYR   0.011   0.001   TYR F 241 
 ARG   0.003   0.000   ARG G 215 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.966 
Fit side-chains
REVERT: F   67 MET cc_start: 0.8487 (mtm) cc_final: 0.8225 (mtm)
REVERT: G   75 ASP cc_start: 0.7395 (t0) cc_final: 0.7194 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 166
  average time/residue: 0.2265
  time to fit residues: 51.5752
Evaluate side-chains
  165 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  212 THR
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  212 THR
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain G residue   61 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 61 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.181867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.116917 restraints weight = 8938.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.86
r_work: 0.2978 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.0961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9029  Z= 0.161
  Angle     :  0.433   7.201  12160  Z= 0.229
  Chirality :  0.035   0.114   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.335  13.398   1221
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 26.28 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.84 (0.25), residues: 1148
  helix:  2.94 (0.16), residues: 1004
  sheet:  None (None), residues: 0
  loop : -0.72 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  18 
 HIS   0.002   0.000   HIS G 136 
 PHE   0.023   0.001   PHE A  32 
 TYR   0.006   0.001   TYR F 241 
 ARG   0.002   0.000   ARG G 215 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 1.012 
Fit side-chains
REVERT: D  128 ASP cc_start: 0.6499 (t0) cc_final: 0.6244 (t0)
REVERT: F   67 MET cc_start: 0.8451 (mtm) cc_final: 0.8196 (mtm)
REVERT: F   83 MET cc_start: 0.7520 (mtt) cc_final: 0.7165 (mtp)
REVERT: G   75 ASP cc_start: 0.7470 (t0) cc_final: 0.7058 (t0)
  outliers start: 10
  outliers final: 4
  residues processed: 160
  average time/residue: 0.2282
  time to fit residues: 49.9759
Evaluate side-chains
  155 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  105 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 93 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 14 optimal weight:    0.2980
   chunk 47 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.182641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.116850 restraints weight = 8785.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.66
r_work: 0.3014 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9029  Z= 0.146
  Angle     :  0.426   6.810  12160  Z= 0.223
  Chirality :  0.035   0.115   1446
  Planarity :  0.004   0.043   1543
  Dihedral  :  3.247  12.745   1221
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 26.06 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.04 (0.25), residues: 1148
  helix:  3.07 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.64 (0.49), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.000   HIS E 136 
 PHE   0.028   0.001   PHE A  32 
 TYR   0.006   0.001   TYR F 241 
 ARG   0.002   0.000   ARG G 215 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.975 
Fit side-chains
REVERT: C  179 MET cc_start: 0.7813 (mpp) cc_final: 0.6757 (mpp)
REVERT: D   64 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7445 (ttmt)
REVERT: D  112 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.4957 (mm)
REVERT: E   85 ASP cc_start: 0.6588 (t70) cc_final: 0.6345 (t0)
REVERT: F   83 MET cc_start: 0.7443 (mtt) cc_final: 0.7077 (mtp)
REVERT: F  165 MET cc_start: 0.9194 (ttp) cc_final: 0.8926 (tmm)
REVERT: G   75 ASP cc_start: 0.7454 (t0) cc_final: 0.7089 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 163
  average time/residue: 0.2286
  time to fit residues: 50.8997
Evaluate side-chains
  164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   64 LYS
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain F residue   51 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 80 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   chunk 81 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 114 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.181881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.117807 restraints weight = 8840.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.78
r_work: 0.2999 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9029  Z= 0.163
  Angle     :  0.431   6.523  12160  Z= 0.226
  Chirality :  0.035   0.120   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.246  12.987   1221
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 26.49 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.06 (0.24), residues: 1148
  helix:  3.08 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.65 (0.48), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.001   HIS G 136 
 PHE   0.026   0.001   PHE A  32 
 TYR   0.006   0.001   TYR F 241 
 ARG   0.002   0.000   ARG G 215 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.911 
Fit side-chains
REVERT: D  100 ILE cc_start: 0.5830 (OUTLIER) cc_final: 0.5440 (pt)
REVERT: D  112 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4916 (mm)
REVERT: E   85 ASP cc_start: 0.6539 (t70) cc_final: 0.6285 (t0)
REVERT: E  218 ILE cc_start: 0.6968 (mp) cc_final: 0.6746 (mp)
REVERT: F   67 MET cc_start: 0.8475 (mtm) cc_final: 0.8197 (mtp)
REVERT: F   83 MET cc_start: 0.7419 (mtt) cc_final: 0.7060 (mtp)
REVERT: F  165 MET cc_start: 0.9243 (ttp) cc_final: 0.8911 (tmm)
REVERT: F  239 LYS cc_start: 0.7143 (mmtm) cc_final: 0.6903 (mmtm)
REVERT: G   75 ASP cc_start: 0.7484 (t0) cc_final: 0.7113 (t0)
  outliers start: 21
  outliers final: 16
  residues processed: 167
  average time/residue: 0.2123
  time to fit residues: 48.5002
Evaluate side-chains
  170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain F residue   51 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0980
   chunk 89 optimal weight:    5.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.184041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.116843 restraints weight = 8761.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.76
r_work: 0.3022 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9029  Z= 0.144
  Angle     :  0.422   6.650  12160  Z= 0.221
  Chirality :  0.035   0.130   1446
  Planarity :  0.003   0.044   1543
  Dihedral  :  3.202  12.591   1221
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.49 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.19 (0.24), residues: 1148
  helix:  3.17 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.64 (0.48), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.000   HIS E 136 
 PHE   0.035   0.001   PHE A  32 
 TYR   0.005   0.001   TYR F 241 
 ARG   0.002   0.000   ARG G 215 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.939 
Fit side-chains
REVERT: C  168 ASN cc_start: 0.7605 (m110) cc_final: 0.7079 (m-40)
REVERT: D  100 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5510 (pt)
REVERT: D  112 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.5042 (mm)
REVERT: E   85 ASP cc_start: 0.6584 (t70) cc_final: 0.6328 (t0)
REVERT: F   67 MET cc_start: 0.8437 (mtm) cc_final: 0.8169 (mtp)
REVERT: F   83 MET cc_start: 0.7444 (mtt) cc_final: 0.7101 (mtp)
REVERT: F  165 MET cc_start: 0.9196 (ttp) cc_final: 0.8837 (tmm)
REVERT: G   75 ASP cc_start: 0.7596 (t0) cc_final: 0.7280 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 166
  average time/residue: 0.2277
  time to fit residues: 51.5476
Evaluate side-chains
  163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain F residue   51 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.183279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.116354 restraints weight = 8862.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.84
r_work: 0.2992 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9029  Z= 0.162
  Angle     :  0.449  11.969  12160  Z= 0.230
  Chirality :  0.035   0.120   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.223  13.053   1221
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 26.17 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.17 (0.24), residues: 1148
  helix:  3.16 (0.16), residues: 999
  sheet:  None (None), residues: 0
  loop : -0.47 (0.48), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.000   HIS G 136 
 PHE   0.022   0.001   PHE A  32 
 TYR   0.008   0.001   TYR F 241 
 ARG   0.002   0.000   ARG F 215 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 1.028 
Fit side-chains
REVERT: C  168 ASN cc_start: 0.7573 (m110) cc_final: 0.7045 (m-40)
REVERT: D  100 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5242 (pt)
REVERT: D  112 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.4888 (mm)
REVERT: D  165 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8218 (tmm)
REVERT: E  106 GLN cc_start: 0.6956 (tp-100) cc_final: 0.6700 (tp40)
REVERT: E  217 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5833 (tt)
REVERT: F   67 MET cc_start: 0.8418 (mtm) cc_final: 0.8161 (mtp)
REVERT: F   83 MET cc_start: 0.7394 (mtt) cc_final: 0.7044 (mtp)
REVERT: F  239 LYS cc_start: 0.7188 (mmtm) cc_final: 0.6987 (mmtm)
REVERT: G   75 ASP cc_start: 0.7599 (t0) cc_final: 0.7254 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 160
  average time/residue: 0.2277
  time to fit residues: 50.0005
Evaluate side-chains
  168 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain F residue   51 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  216 ARG
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 72 optimal weight:    9.9990
   chunk 73 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.179971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.114678 restraints weight = 8986.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.88
r_work: 0.2965 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9029  Z= 0.213
  Angle     :  0.473  11.394  12160  Z= 0.243
  Chirality :  0.036   0.124   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.333  13.651   1221
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 25.96 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.94 (0.24), residues: 1148
  helix:  2.98 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -0.40 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP B  18 
 HIS   0.004   0.001   HIS G 136 
 PHE   0.038   0.001   PHE A  32 
 TYR   0.009   0.001   TYR F 241 
 ARG   0.002   0.000   ARG D 207 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.958 
Fit side-chains
REVERT: D  100 ILE cc_start: 0.5871 (OUTLIER) cc_final: 0.5530 (pt)
REVERT: D  112 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.4901 (mm)
REVERT: D  165 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8362 (tmm)
REVERT: E  217 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5789 (tt)
REVERT: F   83 MET cc_start: 0.7394 (mtt) cc_final: 0.7005 (mtp)
REVERT: G   75 ASP cc_start: 0.7624 (t0) cc_final: 0.7290 (t0)
  outliers start: 24
  outliers final: 19
  residues processed: 162
  average time/residue: 0.2174
  time to fit residues: 48.2284
Evaluate side-chains
  172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  217 LEU
Chi-restraints excluded: chain F residue   51 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  216 ARG
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 90 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.177983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.116115 restraints weight = 8967.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.84
r_work: 0.2909 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9029  Z= 0.259
  Angle     :  0.493   7.043  12160  Z= 0.257
  Chirality :  0.037   0.131   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.468  14.005   1221
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 26.49 %
    Favored  : 70.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.64 (0.24), residues: 1148
  helix:  2.79 (0.16), residues: 1000
  sheet:  None (None), residues: 0
  loop : -0.52 (0.47), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  18 
 HIS   0.005   0.001   HIS G 136 
 PHE   0.037   0.002   PHE A  32 
 TYR   0.011   0.001   TYR F 241 
 ARG   0.003   0.000   ARG F 207 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.756 
Fit side-chains
REVERT: D  100 ILE cc_start: 0.5728 (OUTLIER) cc_final: 0.5309 (pt)
REVERT: D  112 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.5012 (mm)
REVERT: E  148 ASP cc_start: 0.8555 (m-30) cc_final: 0.8333 (m-30)
REVERT: F   83 MET cc_start: 0.7536 (mtt) cc_final: 0.7271 (mtp)
REVERT: G   75 ASP cc_start: 0.7728 (t0) cc_final: 0.7408 (t0)
  outliers start: 24
  outliers final: 16
  residues processed: 165
  average time/residue: 0.2168
  time to fit residues: 48.9985
Evaluate side-chains
  169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain F residue   51 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 47 optimal weight:    7.9990
   chunk 77 optimal weight:    0.8980
   chunk 54 optimal weight:    0.1980
   chunk 53 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.182726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.115636 restraints weight = 8836.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.84
r_work: 0.2982 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9029  Z= 0.148
  Angle     :  0.440   7.139  12160  Z= 0.230
  Chirality :  0.035   0.129   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.300  13.289   1221
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 27.02 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.02 (0.24), residues: 1148
  helix:  3.05 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -0.47 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  18 
 HIS   0.002   0.000   HIS E 136 
 PHE   0.026   0.001   PHE A  32 
 TYR   0.008   0.001   TYR F 241 
 ARG   0.001   0.000   ARG G 215 

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.901 
Fit side-chains
REVERT: D  100 ILE cc_start: 0.5760 (OUTLIER) cc_final: 0.5354 (pt)
REVERT: D  112 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.4926 (mm)
REVERT: F   67 MET cc_start: 0.8500 (mtm) cc_final: 0.8295 (mtp)
REVERT: F   83 MET cc_start: 0.7507 (mtt) cc_final: 0.7121 (mtp)
REVERT: G   75 ASP cc_start: 0.7657 (t0) cc_final: 0.7346 (t0)
  outliers start: 18
  outliers final: 15
  residues processed: 163
  average time/residue: 0.2188
  time to fit residues: 48.9983
Evaluate side-chains
  166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain F residue   51 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 68 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.178233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.113308 restraints weight = 8875.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 1.83
r_work: 0.2924 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2737
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9029  Z= 0.267
  Angle     :  0.507   7.150  12160  Z= 0.264
  Chirality :  0.038   0.151   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.466  13.936   1221
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 27.34 %
    Favored  : 70.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.61 (0.24), residues: 1148
  helix:  2.76 (0.16), residues: 1000
  sheet:  None (None), residues: 0
  loop : -0.48 (0.47), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  18 
 HIS   0.005   0.001   HIS G 136 
 PHE   0.032   0.002   PHE A  32 
 TYR   0.012   0.001   TYR F 241 
 ARG   0.002   0.000   ARG D 207 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5541.22 seconds
wall clock time: 98 minutes 32.12 seconds (5912.12 seconds total)